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changeset 0:4395ea2a01f4 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
author bgruening
date Sat, 06 Feb 2021 10:00:10 +0000
parents
children e8f822eeb9fd
files color_to_gray.py color_to_gray.xml cp_common_functions.py image_math.py macros.xml overlay_outlines.py starting_modules.py starting_modules_groups.xml starting_modules_image.xml starting_modules_images.xml starting_modules_metadata.xml starting_modules_nameandtypes.xml test-data/ExampleHuman.cppipe test-data/color_to_gray.cppipe test-data/color_to_gray_combine_channels.cppipe test-data/color_to_gray_split_channels.cppipe test-data/color_to_gray_split_hsv.cppipe test-data/color_to_gray_split_rgb.cppipe test-data/common-complicated.cppipe test-data/common-nogroup.cppipe test-data/common.cppipe test-data/common_image_math.cppipe test-data/convert_objects_to_image.cppipe test-data/display_data_on_image.cppipe test-data/enhance_or_suppress_features.cppipe test-data/export_to_spreadsheet.cppipe test-data/export_to_spreadsheet_create_gene.cppipe test-data/export_to_spreadsheet_create_gene_image_filename.cppipe test-data/export_to_spreadsheet_create_gene_metadata.cppipe test-data/export_to_spreadsheet_multi.cppipe test-data/gray_to_color.cppipe test-data/identify_primary_objects.cppipe test-data/identify_primary_objects_adv_adaptive_otsu.cppipe test-data/identify_primary_objects_adv_global_manual.cppipe test-data/identify_primary_objects_adv_global_mce.cppipe test-data/identify_primary_objects_adv_global_measurement.cppipe test-data/identify_primary_objects_adv_global_rb.cppipe test-data/identify_primary_objects_noadv.cppipe test-data/image_math.xml test-data/image_math_1.cppipe test-data/image_math_2.cppipe test-data/image_math_3.cppipe test-data/images.tar test-data/images/AS_09125_050116030001_D03f00d0.tif test-data/images/AS_09125_050116030001_D03f00d1.tif test-data/images/AS_09125_050116030001_D03f00d2.tif test-data/mask_image.cppipe test-data/measure_granularity.cppipe test-data/measure_image_area_occupied.cppipe test-data/measure_image_intensity.cppipe test-data/measure_image_quality.cppipe test-data/measure_object_intensity.cppipe test-data/measure_object_size_shape.cppipe test-data/measure_texture.cppipe test-data/overlay_outlines.cppipe test-data/overlay_outlines_blank_color.cppipe test-data/overlay_outlines_blank_grayscale.cppipe test-data/overlay_outlines_non_blank_color.cppipe test-data/overlay_outlines_non_blank_grayscale.cppipe test-data/relate_objects.cppipe test-data/save_images.cppipe test-data/tile.cppipe test-data/tile_across_cycles.cppipe test-data/tile_across_cyles.cppipe test-data/track_object.cppipe test-data/track_object_distance_no_filter_min.cppipe test-data/track_object_follow_neighbors.cppipe test-data/track_object_lap_velocity.cppipe test-data/track_object_measurement_intensity.cppipe test-data/track_object_overlap_no_filter_max.cppipe tile.py track_objects.py
diffstat 69 files changed, 5814 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/color_to_gray.py	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,159 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+
+from cp_common_functions import get_json_value
+from cp_common_functions import get_pipeline_lines
+from cp_common_functions import get_total_number_of_modules
+from cp_common_functions import INDENTATION
+from cp_common_functions import update_module_count
+from cp_common_functions import write_pipeline
+
+MODULE_NAME = "ColorToGray"
+OUTPUT_FILENAME = "output.cppipe"
+
+
+def build_ctg_header(module_name, module_number):
+    """Creates the first line of a module given the name and module number"""
+    result = "|".join([f"{module_name}:[module_num:{module_number}",
+                       "svn_version:\\'Unknown\\'",
+                       "variable_revision_number:4",
+                       "show_window:True",
+                       "notes:\\x5B\\'Convert the color image to grayscale.\\'\\x5D",
+                       "batch_state:array(\\x5B\\x5D, dtype=uint8)",
+                       "enabled:True",
+                       "wants_pause:False]\n"])
+    return result
+
+
+def build_main_block(input_params):
+    """Creates the main block of the CP pipeline with the parameters that don't depend on conditional choices"""
+    result = INDENTATION.join([f"{INDENTATION}Select the input image:{get_json_value(input_params,'name_input_image')}\n",
+                               f"Conversion method:{get_json_value(input_params,'con_conversion_method.conversion_method')}\n",
+                               f"Image type:{get_json_value(input_params,'con_conversion_method.con_image_type.image_type')}\n",
+                               ])
+
+    conversion_method = get_json_value(input_params, 'con_conversion_method.conversion_method')
+
+    image_type = get_json_value(input_params, 'con_conversion_method.con_image_type.image_type')
+    rgb_comb_name_out = "OrigGray"
+    combine_w_red = 1.0
+    combine_w_green = 1.0
+    combine_w_blue = 1.0
+
+    split_red = "Yes"
+    split_green = "Yes"
+    split_blue = "Yes"
+    red_output_name = "OrigRed"
+    green_output_name = "OrigGreen"
+    blue_output_name = "OrigBlue"
+
+    split_hue = "Yes"
+    split_saturation = "Yes"
+    split_value = "Yes"
+    hue_output_name = "OrigHue"
+    saturation_output_name = "OrigSaturation"
+    value_output_name = "OrigValue"
+
+    channel_count = 1
+    if conversion_method == "Combine":
+        if image_type == "RGB" or image_type == "HSV":
+            rgb_comb_name_out = get_json_value(input_params, 'con_conversion_method.name_output_image')
+            combine_w_red = get_json_value(input_params, 'con_conversion_method.con_image_type.weight_red_channel')
+            combine_w_green = get_json_value(input_params, 'con_conversion_method.con_image_type.weight_green_channel')
+            combine_w_blue = get_json_value(input_params, 'con_conversion_method.con_image_type.weight_blue_channel')
+    elif conversion_method == "Split":
+        if image_type == "RGB":
+            split_red = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_red.yes_no')
+            red_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_red.name_output_image')
+            split_green = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_green.yes_no')
+            green_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_green.name_output_image')
+            split_blue = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_blue.yes_no')
+            blue_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_blue.name_output_image')
+        elif image_type == "HSV":
+            split_hue = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_hue.yes_no')
+            hue_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_hue.name_output_image')
+            split_saturation = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_saturation.yes_no')
+            saturation_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_saturation.name_output_image')
+            split_value = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_value.yes_no')
+            value_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_value.name_output_image')
+
+    result += INDENTATION.join(
+        [f"{INDENTATION}Name the output image:{rgb_comb_name_out}\n",
+         f"Relative weight of the red channel:{str(combine_w_red)}\n",
+         f"Relative weight of the green channel:{str(combine_w_green)}\n",
+         f"Relative weight of the blue channel:{str(combine_w_blue)}\n",
+
+         f"Convert red to gray?:{split_red}\n",
+         f"Name the output image:{red_output_name}\n",
+         f"Convert green to gray?:{split_green}\n",
+         f"Name the output image:{green_output_name}\n",
+         f"Convert blue to gray?:{split_blue}\n",
+         f"Name the output image:{blue_output_name}\n",
+
+         f"Convert hue to gray?:{split_hue}\n",
+         f"Name the output image:{hue_output_name}\n",
+         f"Convert saturation to gray?:{split_saturation}\n",
+         f"Name the output image:{saturation_output_name}\n",
+         f"Convert value to gray?:{split_value}\n",
+         f"Name the output image:{value_output_name}\n"
+         ])
+
+    channel_count = 1
+    if image_type == "Channels":
+        channels = input_params['con_conversion_method']['con_image_type']['rpt_channel']
+        channel_count = len(channels)
+        result += INDENTATION.join(
+            [f"{INDENTATION}Channel count:{channel_count}\n"
+             ])
+
+        for ch in channels:
+            rel_weight_ch = 1.0
+            image_name = "Channel1"
+            if conversion_method == "Combine":
+                rel_weight_ch = get_json_value(ch, 'weight_of_channel')
+            else:
+                image_name = get_json_value(ch, 'image_name')
+            result += INDENTATION.join(
+                [f"{INDENTATION}Channel number:{get_json_value(ch,'channel_no')}\n",
+                 f"Relative weight of the channel:{str(rel_weight_ch)}\n",
+                 f"Image name:{image_name}\n"
+                 ])
+    else:
+        result += INDENTATION.join(
+            [f"{INDENTATION}Channel count:{channel_count}\n",
+             "Channel number:Red\\x3A 1\n",
+             "Relative weight of the channel:1.0\n",
+             "Image name:Channel1\n"
+             ])
+
+    return result
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        '-p', '--pipeline',
+        help='CellProfiler pipeline'
+    )
+    parser.add_argument(
+        '-i', '--inputs',
+        help='JSON inputs from Galaxy'
+    )
+    args = parser.parse_args()
+
+    pipeline_lines = get_pipeline_lines(args.pipeline)
+    inputs_galaxy = json.load(open(args.inputs, "r"))
+
+    current_module_num = get_total_number_of_modules(pipeline_lines)
+    current_module_num += 1
+    pipeline_lines = update_module_count(pipeline_lines, current_module_num)
+
+    header_block = build_ctg_header(MODULE_NAME, current_module_num)
+    main_block = build_main_block(inputs_galaxy)
+
+    module_pipeline = f"\n{header_block}{main_block}\n"
+    pipeline_lines.append(module_pipeline)
+
+    write_pipeline(OUTPUT_FILENAME, pipeline_lines)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/color_to_gray.xml	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,289 @@
+<tool id="cp_color_to_gray" name="ColorToGray" version="@CP_VERSION@" python_template_version="3.5">
+    <description> converts color and channel-stacked images to grayscale</description>
+    <macros>
+        <import>macros.xml</import>
+        <xml name="combine_weight">
+            <param name="weight_red_channel" value="1.0" min = "0.0" max = "1.0" type="float" label="Relative weight of the red channel" />
+            <param name="weight_green_channel" value="1.0" min = "0.0" max = "1.0" type="float" label="Relative weight of the green channel" />
+            <param name="weight_blue_channel" value="1.0" min = "0.0" max = "1.0" type="float" label="Relative weight of the blue channel" />
+        </xml>
+        <xml name="image_type_param">
+            <param name="image_type" label="Image type" type="select">
+                <option value="RGB">RGB</option>
+                <option value="HSV">HSV</option>
+                <option value="Channels">Channels</option>
+            </param>
+        </xml>
+
+        <xml name="split_rgb">
+            <conditional name="con_convert_red">
+                <param name="yes_no" type="select" label="Convert red to gray">
+                    <option value="Yes">Yes</option>
+                    <option value="No">No</option>
+                </param>
+                <when value="Yes">
+                    <param name="name_output_image" value="OrigRed" type="text" label="Name the output image" />
+                </when>
+                <when value="No">
+                </when>
+            </conditional>
+            <conditional name="con_convert_green">
+                <param name="yes_no" type="select" label="Convert green to gray">
+                    <option value="Yes">Yes</option>
+                    <option value="No">No</option>
+                </param>
+                <when value="Yes">
+                    <param name="name_output_image" value="OrigGreen" type="text" label="Name the output image" />
+                </when>
+                <when value="No">
+                </when>
+            </conditional>
+            <conditional name="con_convert_blue">
+                <param name="yes_no" type="select" label="Convert blue to gray">
+                    <option value="Yes">Yes</option>
+                    <option value="No">No</option>
+                </param>
+                <when value="Yes">
+                    <param name="name_output_image" value="OrigBlue" type="text" label="Name the output image" />
+                </when>
+                <when value="No">
+                </when>
+            </conditional>
+        </xml>
+
+        <xml name="split_hsv">
+            <conditional name="con_convert_hue">
+                <param name="yes_no" type="select" label="Convert hue to gray">
+                    <option value="Yes">Yes</option>
+                    <option value="No">No</option>
+                </param>
+                <when value="Yes">
+                    <param name="name_output_image" value="OrigHue" type="text" label="Name the output image" />
+                </when>
+                <when value="No">
+                </when>
+            </conditional>
+            <conditional name="con_convert_saturation">
+                <param name="yes_no" type="select" label="Convert saturation to gray">
+                    <option value="Yes">Yes</option>
+                    <option value="No">No</option>
+                </param>
+                <when value="Yes">
+                    <param name="name_output_image" value="OrigSaturation" type="text" label="Name the output image" />
+                </when>
+                <when value="No">
+                </when>
+            </conditional>
+            <conditional name="con_convert_value">
+                <param name="yes_no" type="select" label="Convert value to gray">
+                    <option value="Yes">Yes</option>
+                    <option value="No">No</option>
+                </param>
+                <when value="Yes">
+                    <param name="name_output_image" value="OrigValue" type="text" label="Name the output image" />
+                </when>
+                <when value="No">
+                </when>
+            </conditional>
+        </xml>
+
+        <xml name="combine">
+            <param name="name_output_image" label="Name the output image" value="OrigGray" type="text">
+                <expand macro="text_validator" />
+            </param>
+            <conditional name="con_image_type">
+                <expand macro="image_type_param" />
+                <when value="RGB">
+                    <expand macro="combine_weight"/>
+                </when>
+                <when value="HSV">
+                    <expand macro="combine_weight"/>
+                </when>
+                <when value="Channels">
+                    <repeat name="rpt_channel" title="another channel" min="1">
+                        <param name="channel_no" value="1" type="integer" label="Channel number" />
+                        <param name="weight_of_channel" value="1.0" type="float" min = "0.0" max = "1.0" label="Relative weight of the channel" />
+                    </repeat>
+                </when>
+            </conditional>
+        </xml>
+        <xml name="split">
+            <conditional name="con_image_type">
+                <expand macro="image_type_param" />
+                <when value="RGB">
+                    <expand macro="split_rgb"/>
+                </when>
+                <when value="HSV">
+                    <expand macro="split_hsv"/>
+                </when>
+                <when value="Channels">
+                    <repeat name="rpt_channel" title="another channel" min="1">
+                        <param name="channel_no" value="1" type="integer" label="Channel number" help="This setting chooses a channel to be processed. The channel number should be within the range of channels in the image."/>
+                        <param name="image_name" type="text" label="Image name" />
+                    </repeat>
+                </when>
+            </conditional>
+        </xml>
+
+    </macros>
+    <expand macro="py_requirements"/>
+    <command detect_errors="exit_code">
+        <![CDATA[
+            python '$__tool_directory__/color_to_gray.py' -p '$input_pipeline' -i '$input_json'
+            ]]>
+    </command>
+    <configfiles>
+        <inputs name="input_json"/>
+    </configfiles>
+    <inputs>
+        <expand macro="input_pipeline_param"/>
+        <param name="name_input_image" label="Enter the name of the input image" value="DNA" type="text">
+            <expand macro="text_validator" />
+        </param>
+        <conditional name="con_conversion_method">
+            <param name="conversion_method" type="select" label="Conversion method" >
+                <help>
+                    <![CDATA[
+                        How do you want to convert the color image? 
+                        <i>Split:</i> Splits the channels of a color image (e.g., red, green, blue) into separate grayscale images. 
+                        <i>Combine:</i> Converts a color image to a grayscale image by combining channels together (e.g., red, green, blue).
+                    ]]>
+
+                </help>
+                <option value="Combine">Combine</option>
+                <option value="Split">Split</option>
+            </param>
+            <when value="Combine">
+                <expand macro="combine"/>
+            </when>
+            <when value="Split">
+                <expand macro="split"/>
+            </when>
+        </conditional>
+        
+    </inputs>
+    <outputs>
+        <expand macro="output_pipeline_param" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_pipeline" value="common.cppipe"/>
+            <param name="name_input_image" value="OrigColor" />
+            <conditional name="con_conversion_method">
+                <param name="conversion_method" value="Combine"/>
+                <param name="name_output_image" value="OrigGray" />
+                <conditional name="con_image_type">
+                    <param name = "image_type" value="RGB"/>
+                    <param name ="weight_red_channel" value = "1.0" />
+                    <param name ="weight_green_channel" value = "1.0" />
+                    <param name ="weight_blue_channel" value = "1.0" />
+                </conditional>
+            </conditional>
+            <expand macro="test_out_file" file="color_to_gray.cppipe" />
+        </test>
+        <test>
+            <param name="input_pipeline" value="common.cppipe"/>
+            <param name="name_input_image" value="DNA" />
+            <conditional name="con_conversion_method">
+                <param name="conversion_method" value="Combine"/>
+                <param name="name_output_image" value="OrigGray" />
+                <conditional name="con_image_type">
+                    <param name = "image_type" value="Channels"/>
+                    <repeat name="rpt_channel">
+                        <param name="channel_no" value="2" />
+                        <param name="weight_of_channel" value="0.2" />
+                    </repeat>
+                    <repeat name="rpt_channel">
+                        <param name="channel_no" value="3" />
+                        <param name="weight_of_channel" value="0.5" />
+                    </repeat>
+                </conditional>
+            </conditional>
+
+            <expand macro="test_out_file" file="color_to_gray_combine_channels.cppipe" />
+        </test>
+        <test>
+            <param name="input_pipeline" value="common.cppipe"/>
+            <param name="name_input_image" value="DNA" />
+            <conditional name="con_conversion_method">
+                <param name="conversion_method" value="Split"/>
+                <param name="name_output_image" value="OrigGray" />
+                <conditional name="con_image_type">
+                    <param name = "image_type" value="HSV"/>
+                    <conditional name="con_convert_hue">
+                        <param name="yes_no" value="Yes" />
+                        <param name="name_output_image" value="OutputHue" />
+                    </conditional>
+                    <conditional name="con_convert_saturation">
+                        <param name="yes_no" value="No" />
+                    </conditional>
+                    <conditional name="con_convert_value">
+                        <param name="yes_no" value="Yes" />
+                        <param name="name_output_image" value="OutputValue" />
+                    </conditional>
+                </conditional>
+            </conditional>
+
+            <expand macro="test_out_file" file="color_to_gray_split_hsv.cppipe" />
+        </test>
+        <test>
+            <param name="input_pipeline" value="common.cppipe"/>
+            <param name="name_input_image" value="DNA" />
+            <conditional name="con_conversion_method">
+                <param name="conversion_method" value="Split"/>
+                <param name="name_output_image" value="DNA" />
+                <conditional name="con_image_type">
+                    <param name = "image_type" value="RGB"/>
+                    <conditional name="con_convert_red">
+                        <param name="yes_no" value="Yes" />
+                        <param name="name_output_image" value="OutputRed" />
+                    </conditional>
+                    <conditional name="con_convert_green">
+                        <param name="yes_no" value="Yes" />
+                        <param name="name_output_image" value="OutputGreen" />
+                    </conditional>
+                    <conditional name="con_convert_blue">
+                        <param name="yes_no" value="No" />
+                        
+                    </conditional>
+                </conditional>
+            </conditional>
+
+            <expand macro="test_out_file" file="color_to_gray_split_rgb.cppipe" />
+        </test>
+        <test>
+            <param name="input_pipeline" value="common.cppipe"/>
+            <param name="name_input_image" value="DNA" />
+            <conditional name="con_conversion_method">
+                <param name="conversion_method" value="Split"/>
+                <param name="name_output_image" value="DNA" />
+                <conditional name="con_image_type">
+                    <param name = "image_type" value="Channels"/>
+                    <repeat name="rpt_channel">
+                        <param name="channel_no" value="2" />
+                        <param name="image_name" value="Image2" />
+                    </repeat>
+                    <repeat name="rpt_channel">
+                        <param name="channel_no" value="3" />
+                        <param name="image_name" value="Image3" />
+                    </repeat>
+                </conditional>
+            </conditional>
+
+            <expand macro="test_out_file" file="color_to_gray_split_channels.cppipe" />
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+
+            .. class:: infomark
+
+            **What it does**
+
+            This module converts color and channel-stacked images to grayscale. All channels can be merged into one grayscale image (Combine), or each channel can be extracted into a separate grayscale image (Split). If you use Combine, the relative weights you provide allow adjusting the contribution of the colors relative to each other. Note that all Identify modules require grayscale images. 
+
+            @COMMON_HELP@
+            ]]>
+    </help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cp_common_functions.py	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,62 @@
+INDENTATION = "    "
+LINE_NUM_MODULES = 4
+
+
+def get_json_value(json_input, keys_path):
+    """Returns the value specified in keys_path (using dot notation) or an empty string if the key doesn't exist"""
+    if not isinstance(json_input, dict):
+        return ""
+    keys = keys_path.split(".")
+    try:
+        value = json_input[keys[0]]
+        for key in keys[1:]:
+            value = value[key]
+        return value
+    except KeyError:
+        return ""
+
+
+def concat_conditional(a, b):
+    if a == "" or b == "":
+        return ""
+    else:
+        return f"{a}_{b}"
+
+
+def get_total_number_of_modules(pipeline_lines):
+    """Gets the number of modules from the header of the previous pipeline"""
+    number_of_modules = pipeline_lines[LINE_NUM_MODULES].strip().split(':')[1]
+    return int(number_of_modules)
+
+
+def get_pipeline_lines(input_pipeline):
+    """Returns a list with the lines in the .cppipe file"""
+    with open(input_pipeline) as f:
+        lines = f.readlines()
+    return lines
+
+
+def update_module_count(pipeline_lines, count):
+    """Updates the number of modules in the .cppipe header"""
+    module_count_entry = pipeline_lines[LINE_NUM_MODULES].strip().split(':')[0]
+    pipeline_lines[4] = f"{module_count_entry}:{count}\n"
+    return pipeline_lines
+
+
+def write_pipeline(filename, lines_pipeline):
+    """Writes the lines composing the pipeline into a file"""
+    with open(filename, "w") as f:
+        f.writelines(lines_pipeline)
+
+
+def build_header(module_name, module_number):
+    """Creates the first line of a module given the name and module number"""
+    result = "|".join([f"{module_name}:[module_num:{module_number}",
+                       "svn_version:\\'Unknown\\'",
+                       "variable_revision_number:4",
+                       "show_window:False",
+                       "notes:\\x5B\\x5D",
+                       "batch_state:array(\\x5B\\x5D, dtype=uint8)",
+                       "enabled:True",
+                       "wants_pause:False]\n"])
+    return result
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/image_math.py	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,135 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+
+from cp_common_functions import build_header
+from cp_common_functions import concat_conditional
+from cp_common_functions import get_json_value
+from cp_common_functions import get_pipeline_lines
+from cp_common_functions import get_total_number_of_modules
+from cp_common_functions import INDENTATION
+from cp_common_functions import update_module_count
+from cp_common_functions import write_pipeline
+
+MODULE_NAME = "ImageMath"
+OUTPUT_FILENAME = "output.cppipe"
+
+operator_map = {
+    "add": "Add",
+    "subtract": "Subtract",
+    "multiply": "Multiply",
+    "divide": "Divide",
+    "average": "Average",
+    "minimum": "Minimum",
+    "maximum": "Maximum",
+    "invert": "Invert",
+    "log_2": "Log transform (base 2)",
+    "log_legacy": "Log transform (legacy)",
+    "and": "And",
+    "or": "Or",
+    "not": "Not",
+    "equals": "Equals"
+}
+
+
+def build_main_block(input_params):
+    """Creates the main block of the CP pipeline with the parameters that don't depend on conditional choices"""
+    operation = operator_map[get_json_value(
+        input_params, 'operation.operation')]
+    result = INDENTATION.join([f"{INDENTATION}Operation:{operation}\n",
+                               f"Raise the power of the result by:{get_json_value(input_params,'operation.op_results.raise_the_power_of_the_result_by')}\n",
+                               f"Multiply the result by:{get_json_value(input_params,'operation.op_results.multiply_the_result_by')}\n",
+                               f"Add to result:{get_json_value(input_params,'operation.op_results.add_to_result')}\n",
+                               f"Set values less than 0 equal to 0?:{get_json_value(input_params,'operation.op_results.set_values_less_than_0_equal_to_0')}\n",
+                               f"Set values greater than 1 equal to 1?:{get_json_value(input_params,'operation.op_results.set_values_greater_than_1_equal_to_1')}\n",
+                               f"Ignore the image masks?:{get_json_value(input_params,'ignore_the_image_masks')}\n",
+                               f"Name the output image:{get_json_value(input_params,'name_output_image')}"
+                               ])
+    return result
+
+
+def build_variable_block(inputs_galaxy):
+    result = ""
+    first_image_block = build_first_image_block(
+        get_json_value(inputs_galaxy, 'operation.first_image'))
+    result += f"\n{first_image_block}"
+    second_image_block = build_second_image_block(
+        get_json_value(inputs_galaxy, 'operation.second_image'))
+    result += f"\n{second_image_block}"
+    return result
+
+
+def build_first_image_block(input_params):
+    """Creates the block of parameters for the first operator in operations"""
+
+    value_select = get_json_value(
+        input_params, 'image_or_measurement_first.image_or_measurement_first')
+    image_name = get_json_value(
+        input_params, 'image_or_measurement_first.select_the_first_image')
+    value_multiply = get_json_value(
+        input_params, 'multiply_the_first_image_by')
+    category = get_json_value(
+        input_params, 'image_or_measurement_first.category_first.category_first')
+    measurement = get_json_value(
+        input_params, 'image_or_measurement_first.category_first.measurement_first')
+
+    result = INDENTATION.join(
+        [f"{INDENTATION}Image or measurement?:{value_select}\n",
+         f"Select the first image:{image_name}\n",
+         f"Multiply the first image by:{value_multiply}\n",
+         f"Measurement:{concat_conditional(category, measurement)}"
+         ])
+    return result
+
+
+def build_second_image_block(input_params):
+    """Creates the block of parameters for the second operator in binary operations"""
+
+    value_select = get_json_value(
+        input_params, 'image_or_measurement_second.image_or_measurement_second')
+    image_name = get_json_value(
+        input_params, 'image_or_measurement_second.select_the_second_image')
+    value_multiply = get_json_value(
+        input_params, 'multiply_the_second_image_by')
+    category = get_json_value(
+        input_params, 'image_or_measurement_second.category_second.category_second')
+    measurement = get_json_value(
+        input_params, 'image_or_measurement_second.category_second.measurement_second')
+
+    result = INDENTATION.join(
+        [f"{INDENTATION}Image or measurement?:{value_select}\n",
+         f"Select the second image:{image_name}\n",
+         f"Multiply the second image by:{value_multiply}\n",
+         f"Measurement:{concat_conditional(category, measurement)}"
+         ])
+    return result
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        '-p', '--pipeline',
+        help='CellProfiler pipeline'
+    )
+    parser.add_argument(
+        '-i', '--inputs',
+        help='JSON inputs from Galaxy'
+    )
+    args = parser.parse_args()
+
+    pipeline_lines = get_pipeline_lines(args.pipeline)
+    inputs_galaxy = json.load(open(args.inputs, "r"))
+
+    current_module_num = get_total_number_of_modules(pipeline_lines)
+    current_module_num += 1
+    pipeline_lines = update_module_count(pipeline_lines, current_module_num)
+
+    header_block = build_header(MODULE_NAME, current_module_num)
+    main_block = build_main_block(inputs_galaxy)
+    variable_block = build_variable_block(inputs_galaxy)
+
+    module_pipeline = f"\n{header_block}{main_block}{variable_block}\n"
+    pipeline_lines.append(module_pipeline)
+
+    write_pipeline(OUTPUT_FILENAME, pipeline_lines)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,93 @@
+<macros>
+    <token name="@CP_VERSION@">3.1.9</token>
+    <token name="@PY_VERSION@">3.7</token>
+    <token name="@FORMATS@">jpg,png,tiff,bmp,gif,pcx,ppm,psd,pbm,pgm,eps</token>
+    <token name="@SPACES@">"    "</token>
+    <!-- four spaces needed for CP pipeline file -->
+    <token name="@COMMON_HELP@">
+        .. class:: infomark
+
+        **Input**
+
+        Existing CellProfiler pipeline file *(.cppipe)* or generated by linking CellProfiler tools.
+
+        .. class:: infomark
+
+        **Output**
+
+        The input CellProfiler pipeline file *(.cppipe)* in addition to the settings of this module.
+
+        .. class:: warningmark
+
+        **IMPORTANT**
+
+        The first tool in a CellProfiler workflow has to be **Starting modules** and the last one **CellProfiler**. You can also execute the entire pipeline with the final CellProfiler tool, in which you feed in the images you want to process as well.
+    </token>
+
+
+    <xml name="output_pipeline_param">
+        <data name="output_pipeline" from_work_dir="output.cppipe" format="txt"/>
+    </xml>
+
+
+    <xml name="input_pipeline_param">
+        <param name="input_pipeline" type="data" format="data" label="Select the input CellProfiler pipeline"/>
+    </xml>
+
+
+    <xml name="cp_requirements">
+        <requirements>
+            <requirement type="package" version="@CP_VERSION@">cellprofiler</requirement>
+        </requirements>
+    </xml>
+
+
+    <xml name="py_requirements">
+        <requirements>
+            <requirement type="package" version="@PY_VERSION@">python</requirement>
+        </requirements>
+    </xml>
+
+
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @article{McQuin_2018,
+                title = {CellProfiler 3.0: Next-generation image processing for biology},
+                author = {McQuin C, Goodman A, Chernyshev V, Kamentsky L, Cimini BA, Karhohs KW, Doan M, Ding L, Rafelski SM, Thirstrup D, Wiegraebe W, Singh S, Becker T, Caicedo JC, Carpenter AE},
+                year = {2018},
+                volume = {16(7):e2005970},
+                DOI = {10.1371/journal.pbio.2005970},
+                journal = {PLoS Biol.},
+                url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005970},
+                }
+            </citation>
+        </citations>
+    </xml>
+
+
+    <xml name="cmd_modules">
+        <command detect_errors="aggressive">
+            <![CDATA[
+                python '$script_file' '$inputs' '$input_pipeline'
+                ]]>
+        </command>
+    </xml>
+
+
+    <xml name="text_validator">
+        <validator type="regex" message="Only numbers, letters, hyphen, underscore and spaces are allowed">^[A-Za-z0-9 _-]*$</validator>
+    </xml>
+
+
+    <xml name="test_input_pipeline_param">
+        <param name="input_pipeline" value="common.cppipe" />
+    </xml>
+
+
+    <xml name="test_out_file" token_file="common.cppipe">
+        <output name="output_pipeline" ftype="txt" file="@FILE@" lines_diff="0"/>
+    </xml>
+    
+</macros>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/overlay_outlines.py	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,109 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+
+from cp_common_functions import get_json_value
+from cp_common_functions import get_pipeline_lines
+from cp_common_functions import get_total_number_of_modules
+from cp_common_functions import INDENTATION
+from cp_common_functions import update_module_count
+from cp_common_functions import write_pipeline
+
+MODULE_NAME = "OverlayOutlines"
+OUTPUT_FILENAME = "output.cppipe"
+
+
+def build_ctg_header(module_name, module_number):
+    """Creates the first line of a module given the name and module number"""
+    result = "|".join([f"{module_name}:[module_num:{module_number}",
+                       "svn_version:\\'Unknown\\'",
+                       "variable_revision_number:4",
+                       "show_window:True",
+                       "notes:\\x5B\\'Overlay the embryo outlines on the grayscale image.\\'\\x5D",
+                       "batch_state:array(\\x5B\\x5D, dtype=uint8)",
+                       "enabled:True",
+                       "wants_pause:False]\n"])
+    return result
+
+
+def build_main_block(input_params):
+    result = f"{INDENTATION}Display outlines on a blank image?:{get_json_value(input_params,'con_blank_img.blank_img')}\n"
+
+    on_blank = get_json_value(input_params, 'con_blank_img.blank_img')
+    # defaults
+    img_to_display = "None"
+    display_mode = get_json_value(input_params, 'con_blank_img.con_display_mode.display_mode')
+    method_brightness = "Max of image"
+    howto = get_json_value(input_params, 'howto_outline')
+    outline_color = "#FF0000"
+    obj_to_display = "None"
+
+    name_output_img = get_json_value(input_params, 'name_output_image')
+
+    if on_blank == "No":
+        img_to_display = get_json_value(input_params, 'con_blank_img.image_to_outline')
+
+    result += INDENTATION.join(
+        [f"{INDENTATION}Select image on which to display outlines:{img_to_display}\n",
+         f"Name the output image:{name_output_img}\n",
+         f"Outline display mode:{display_mode}\n"
+         ])
+
+    if on_blank == "No" and display_mode == "Grayscale":
+        method_brightness = get_json_value(input_params, 'con_blank_img.con_display_mode.method_brightness')
+
+    result += INDENTATION.join(
+        [f"{INDENTATION}Select method to determine brightness of outlines:{method_brightness}\n",
+         f"How to outline:{howto}\n"
+         ])
+
+    obj_outline_str = ""
+
+    if display_mode == "Color":
+        for obj in input_params['con_blank_img']['con_display_mode']['rpt_obj_to_display']:
+            outline_color = get_json_value(obj, 'outline_color')
+            obj_to_display = get_json_value(obj, 'obj_to_display')
+            obj_outline_str += INDENTATION.join(
+                [f"{INDENTATION}Select outline color:{outline_color}\n",
+                 f"Select objects to display:{obj_to_display}\n"
+                 ])
+    else:  # grayscale
+        for obj in input_params['con_blank_img']['con_display_mode']['rpt_obj_to_display']:
+            obj_to_display = get_json_value(obj, 'obj_to_display')
+            obj_outline_str += INDENTATION.join(
+                [f"{INDENTATION}Select outline color:{outline_color}\n",
+                 f"Select objects to display:{obj_to_display}\n"
+                 ])
+    obj_outline_str = obj_outline_str.rstrip("\n")
+    result += f"{obj_outline_str}"
+
+    return result
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        '-p', '--pipeline',
+        help='CellProfiler pipeline'
+    )
+    parser.add_argument(
+        '-i', '--inputs',
+        help='JSON inputs from Galaxy'
+    )
+    args = parser.parse_args()
+
+    pipeline_lines = get_pipeline_lines(args.pipeline)
+    inputs_galaxy = json.load(open(args.inputs, "r"))
+
+    current_module_num = get_total_number_of_modules(pipeline_lines)
+    current_module_num += 1
+    pipeline_lines = update_module_count(pipeline_lines, current_module_num)
+
+    header_block = build_ctg_header(MODULE_NAME, current_module_num)
+    main_block = build_main_block(inputs_galaxy)
+
+    module_pipeline = f"\n{header_block}{main_block}\n"
+    pipeline_lines.append(module_pipeline)
+
+    write_pipeline(OUTPUT_FILENAME, pipeline_lines)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/starting_modules.py	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,223 @@
+import json
+import sys
+
+FOURSPACES = "    "
+
+input_json_path = sys.argv[1]
+
+params = json.load(open(input_json_path, "r"))
+
+
+def write_images():
+    filter_images = params['images']['filter_images']
+
+    _str = "\nImages:[module_num:1|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
+    _str += FOURSPACES + ":\n"
+    _str += FOURSPACES + "Filter images?:%s\n" % filter_images
+    _str += FOURSPACES + "Select the rule criteria:and (extension does isimage) (directory doesnot startwith \".\")\n"
+
+    return _str
+
+
+def write_metadata():
+    metadata_extraction = params['metadata']['con_metadata_extraction']
+    extract = metadata_extraction['extract']
+
+    if 'extraction_method' in metadata_extraction:
+        method_count = len(metadata_extraction['extraction_method'])
+    else:
+        method_count = 1
+
+    _str = "\nMetadata:[module_num:2|svn_version:\\'Unknown\\'|variable_revision_number:4|show_window:False|notes:\\x5B\\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
+    _str += FOURSPACES + "Extract metadata?:%s\n" % extract
+
+    if extract == "No":
+        _str += FOURSPACES + "Metadata data type:Text\n"
+        _str += FOURSPACES + "Metadata types:{}\n"
+        _str += FOURSPACES + "Extraction method count:%d\n" % method_count
+        _str += FOURSPACES + "Metadata extraction method:Extract from file/folder names\n"
+        _str += FOURSPACES + "Regular expression to extract from file name:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)_w(?P<ChannelNumber>\x5B0-9\x5D)\n"
+        _str += FOURSPACES + "Regular expression to extract from folder name:(?P<Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$\n"
+        _str += FOURSPACES + "Extract metadata from:All images\n"
+        _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n"
+        _str += FOURSPACES + "Metadata file location:\n"
+        _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
+        _str += FOURSPACES + "Use case insensitive matching?:No\n"
+    else:
+        _str += FOURSPACES + "Metadata data type:Text\n"  # default Text,not possible to select in Galaxy
+        _str += FOURSPACES + "Metadata types:{}\n"
+        _str += FOURSPACES + "Extraction method count:%d\n" % method_count
+
+        for methods in metadata_extraction["extraction_method"]:
+            _str += FOURSPACES + "Metadata extraction method:%s\n" % methods["metadata_extraction_method"]
+            _str += FOURSPACES + "Metadata source:%s\n" % methods["con_metadata_source"]["metadata_source"]
+
+            if "file_name_regex" in methods["con_metadata_source"]:
+                file_regex = methods["con_metadata_source"]["file_name_regex"]
+                folder_regex = "(?P<folderField1>.*)"
+            elif "folder_name_regex" in methods["con_metadata_source"]:
+                file_regex = "(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)"
+                folder_regex = methods["con_metadata_source"]["folder_name_regex"]
+            else:
+                # default regex
+                file_regex = "(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)"
+                folder_regex = "(?P<folderField1>.*)"
+
+            _str += FOURSPACES + "Regular expression to extract from file name:%s\n" % file_regex
+            _str += FOURSPACES + "Regular expression to extract from folder name:%s\n" % folder_regex
+
+            _str += FOURSPACES + "Extract metadata from:%s\n" % methods["con_metadata_extract_from"]["extract_metadata_from"]
+
+            if methods["con_metadata_extract_from"]["extract_metadata_from"] == "Images matching a rule":
+                rule_str = ""
+                for r in methods["con_metadata_extract_from"]["r_match"]:
+                    if r["con_match"]["rule_type"] == "extension":
+                        rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \
+                                    r["con_match"]["match_type"] + ")"
+                    else:
+                        rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " +\
+                            r["con_match"]["contain"] + " \"" + r["con_match"]["match_value"] + "\")"
+
+                _str += FOURSPACES + "Select the filtering criteria:" + methods["con_metadata_extract_from"]["match_all_any"] + rule_str + "\n"
+            else:
+                _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n"  # this line is required even if it's not used
+
+            _str += FOURSPACES + "Metadata file location:\n"
+            _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
+            _str += FOURSPACES + "Use case insensitive matching?:No\n"
+
+    return _str
+
+
+def write_nameandtypes():
+    nameandtypes = params['nameandtypes']
+    assign_a_name = nameandtypes['con_assign_a_name_to']['assign_a_name_to']
+
+    if "con_select_image_type" in nameandtypes['con_assign_a_name_to']:
+        con_set_intensity = nameandtypes['con_assign_a_name_to']['con_select_image_type']['con_set_intensity']
+        max_intensity = con_set_intensity['maximum_intensity'] if "maximum_intensity" in con_set_intensity else 255.0
+    else:
+        max_intensity = 255.0
+
+    pixel_space = nameandtypes['pixel_space']
+
+    rule_count = len(nameandtypes['con_assign_a_name_to']['r_match_rule']) if "r_match_rule" in nameandtypes['con_assign_a_name_to'] else 1
+
+    process_3d = nameandtypes['pixel_space']['process_3d']
+    x_spacing = 1.0 if "x_spacing" not in pixel_space else pixel_space["x_spacing"]
+    y_spacing = 1.0 if "y_spacing" not in pixel_space else pixel_space["y_spacing"]
+    z_spacing = 1.0 if "z_spacing" not in pixel_space else pixel_space["z_spacing"]
+
+    _str = "\nNamesAndTypes:[module_num:3|svn_version:\\'Unknown\\'|variable_revision_number:8|show_window:False|notes:\\x5B\\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
+
+    _str += FOURSPACES + "Assign a name to:%s\n" % assign_a_name
+
+    if assign_a_name == "All images":
+        _str += FOURSPACES + "Select the image type:%s\n" % nameandtypes['con_assign_a_name_to']['con_select_image_type']['select_image_type']
+        _str += FOURSPACES + "Name to assign these images:%s\n" % nameandtypes['con_assign_a_name_to']['name_to_assign']
+        _str += FOURSPACES + "Match metadata:[]\n"
+
+        _str += FOURSPACES + "Image set matching method:Order\n"
+        _str += FOURSPACES + "Set intensity range from:%s\n" % con_set_intensity['set_intensity_range_from']
+        _str += FOURSPACES + "Assignments count:%s\n" % rule_count
+        _str += FOURSPACES + "Single images count:0\n"
+        _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
+        _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
+
+    else:
+        # the below lines are not relevant to "images matching rules", but needed in pipeline file
+        _str += FOURSPACES + "Select the image type:Grayscale image\n"
+        _str += FOURSPACES + "Name to assign these images:DNA\n"
+        _str += FOURSPACES + "Match metadata:[]\n"
+
+        _str += FOURSPACES + "Image set matching method:%s\n" % nameandtypes['con_assign_a_name_to']['matching_method']
+        _str += FOURSPACES + "Set intensity range from:Image metadata\n"
+        _str += FOURSPACES + "Assignments count:%d\n" % rule_count
+        _str += FOURSPACES + "Single images count:0\n"
+        _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
+        _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
+
+    _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" % x_spacing
+    _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" % y_spacing
+    _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" % z_spacing
+
+    if assign_a_name == "Images matching rules":
+        for rule in nameandtypes["con_assign_a_name_to"]["r_match_rule"]:
+
+            rule_str = ""
+            if len(rule["r_match"]) > 0:
+                for r in rule["r_match"]:
+                    if r["con_match"]["rule_type"] == "file" or r["con_match"]["rule_type"] == "directory":
+                        rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \
+                            r["con_match"]["contain"] + " \"" + r["con_match"]["match_value"] + "\")"
+                    else:
+                        rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \
+                            r["con_match"]["match_type"] + ")"
+            else:
+                rule_str = " (file does contain \"\")"  # need to have a value even if it is not used
+
+            _str += FOURSPACES + "Select the rule criteria:" + rule["match_all_any"] + rule_str + "\n"
+
+            img_or_obj = rule["con_select_image_type"]["select_image_type"]
+
+            if img_or_obj == "Objects":
+                _str += FOURSPACES + "Name to assign these images:DNA\n"
+                _str += FOURSPACES + "Name to assign these objects:%s\n" % rule["con_select_image_type"]["name_to_assign"]
+            else:
+                _str += FOURSPACES + "Name to assign these images:%s\n" % rule["con_select_image_type"]["name_to_assign"]
+                _str += FOURSPACES + "Name to assign these objects:Cell\n"
+
+            _str += FOURSPACES + "Select the image type:%s\n" % img_or_obj
+
+            intensity_range = "Image metadata"  # default value
+            if img_or_obj == "Grayscale image" or img_or_obj == "Color image":
+                intensity_range = rule["con_select_image_type"]["con_set_intensity"]["set_intensity_range_from"]
+
+            _str += FOURSPACES + "Set intensity range from:%s\n" % intensity_range
+
+            if intensity_range == "Manual":
+                _str += FOURSPACES + "Maximum intensity:%s\n" % rule["con_select_image_type"]["con_set_intensity"]["maximum_intensity"]
+            else:
+                _str += FOURSPACES + "Maximum intensity:255.0\n"
+
+    return _str
+
+
+def write_groups():
+    groups = params['groups']
+
+    _str = "\nGroups:[module_num:4|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
+
+    group_images = groups["con_groups"]["group_images"]
+
+    _str += FOURSPACES + "Do you want to group your images?:%s\n" % group_images
+    _str += FOURSPACES + "grouping metadata count:1\n"
+
+    if group_images == "Yes":
+        _str += FOURSPACES + "Metadata category:%s\n" % groups["con_groups"]["group_category"]
+    else:
+        _str += FOURSPACES + "Metadata category:None\n"
+
+    return _str
+
+
+with open("output.cppipe", "w") as f:
+    headers = ["CellProfiler Pipeline: http://www.cellprofiler.org\n",
+               "Version:3\n",
+               "DateRevision:319\n",
+               "GitHash:\n",
+               "ModuleCount:4\n",
+               "HasImagePlaneDetails:False",
+               "\n"]
+
+    f.writelines(headers)
+
+    img_str = write_images()
+    metadata_str = write_metadata()
+    nameandtypes_str = write_nameandtypes()
+    groups_str = write_groups()
+
+    output_str = img_str + metadata_str + nameandtypes_str + groups_str
+
+    f.write(output_str)
+    f.close()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/starting_modules_groups.xml	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,32 @@
+<macros>
+    <xml name="starting_modules_groups">
+        <section name="groups" title="Groups" expanded="false">
+        <conditional name="con_groups">
+            <param name="group_images" type="select" value="No" label="Do you want to group your images?">
+                <option value="Yes">Yes, group the images</option>
+                <option value="No" selected="true">No, do not group images</option>
+            </param>
+            <when value="Yes">
+                <param name="group_category" type="select" label="Metadata category">
+                    <option value="None" selected="true">None</option>
+                    <option value="ChannelNumber">Channel number</option>
+                    <option value="FileLocation">File location</option>
+                    <option value="Plate">Plate</option>
+                    <option value="Frame">Frame</option>
+                    <option value="Series">Series</option>
+                    <option value="Site">Site</option>
+                    <option value="Well">Well</option>
+                    <option value="field1">field1</option>
+                    <option value="field2">field2</option>
+                    <option value="field3">field3</option>
+                    <option value="field4">field4</option>
+                    <option value="field5">field5</option>
+                    <option value="field6">field6</option>
+                </param>
+            </when>
+            <when value="No">
+            </when>
+        </conditional>
+    </section>
+    </xml>
+</macros>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/starting_modules_images.xml	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,10 @@
+<macros>
+    <xml name="starting_modules_images">
+        <section name="images" title="Images" expanded="false">
+            <param name="filter_images" type="select" label="Do you want to filter only the images?" help="Enabling file filtering is useful if, for example, you drag-and-dropped a folder onto the file list panel which contains a mixture of images that you want to analyze and other files that you want to ignore.">
+                <option value="Images only">Select the images only</option>
+                <option value="No filtering">Select all the files</option>
+            </param>
+        </section>
+    </xml>
+</macros>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/starting_modules_metadata.xml	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,92 @@
+<macros>
+    <xml name="image_matching_rules_metadata">
+        <param name="match_all_any" type="select" display="radio" label="Match the following rules">
+            <option value="and">All</option>
+            <option value="or">Any</option>
+        </param>
+        <repeat name="r_match" title="filtering rules">
+            <conditional name="con_match">
+                <param name="rule_type" type="select" label="Select the filtering criteria">
+                    <option value="file">File</option>
+                    <option value="directory">Directory</option>
+                    <option value="extension">Extension</option>
+                </param>
+                <when value="file">
+                    <expand macro="name_type_rule_matching_file"/>
+                </when>
+                <when value="directory">
+                    <expand macro="name_type_rule_matching_file"/>
+                </when>
+                <when value="extension">
+                    <expand macro="name_type_rule_ext" />
+                </when>
+            </conditional>
+        </repeat>
+    </xml>
+    <xml name="starting_modules_metadata">
+        <section name="metadata" title="Metadata" expanded="false">
+            <conditional name="con_metadata_extraction">
+                <param name="extract" type="select" label="Do you want to extract the metadata?">
+                    <option value="Yes">Yes, specify metadata</option>
+                    <option value="No" selected="true">No, do not specify metadata</option>
+                </param>
+                <when value="Yes">
+                    <repeat name="extraction_method" title="new metadata" min="1">
+                        <param name="metadata_extraction_method" type="select" label="Metadata extraction method" help="Metadata can be stored in either or both of two ways: internally (through the file naming, directory structuring, or the file header information) or externally (external index, such as spreadsheet or database of some kind). " >
+                            <option value="Extract from file/folder names">Extract from file/folder names</option>
+                            <option value="Import from file">Import from file</option>
+                            <option value="Extract from image file headers">Extract from image file headers</option>
+                        </param>
+                        <conditional name="con_metadata_source">
+                            <param name="metadata_source" type="select" label="Metadata source" help="You can extract the metadata from the image file name or from its folder name.">
+                                <option value="File name">File name</option>
+                                <option value="Folder name">Folder name</option>
+                            </param>
+                            <when value="File name">
+                                <param name="file_name_regex" type="select" label="Select the pattern to extract metadata from the file name" help="Image file names must comply with one of the patterns. For example, plate_reagent_timepoint.tif matches the pattern field1_field2_field3. If none of the patterns is suitable, please use other Galaxy tools to rename your files first.">
+
+                                    <sanitizer sanitize="false"/>
+                                    <option value="(?P&lt;field1>.*)">field1</option>
+                                    <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)">field1-field2</option>
+                                    <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)">field1_field2</option>
+                                    <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)">field1__field2</option>
+                                    <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)">field1-field2-field3</option>
+                                    <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)">field1_field2_field3</option>
+                                    <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)">field1__field2__field3</option>
+                                    <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)">field1-field2-field3-field4</option>
+                                    <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)">field1_field2_field3_field4</option>
+                                    <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)">field1__field2__field3__field4</option>
+                                    <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)-(?P&lt;field5>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5</option>
+                                    <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)_(?P&lt;field5>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5</option>
+                                    <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)__(?P&lt;field5>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5</option>
+                                    <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)-(?P&lt;field5>[a-zA-Z0-9]+)-(?P&lt;field6>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5-field6</option>
+                                    <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)_(?P&lt;field5>[a-zA-Z0-9]+)_(?P&lt;field6>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5_field6</option>
+                                    <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)__(?P&lt;field5>[a-zA-Z0-9]+)__(?P&lt;field6>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5__field6</option>
+                                </param>
+                            </when>
+                            <when value="Folder name">
+                                <param name="folder_name_regex" type="select" label="Select the pattern to extract metadata from the folder name" help="Folder names must comply with one of the patterns. For example, folder name exp1-channel_name matches the pattern field1-field2. If none of the patterns is suitable, please use other Galaxy tools to rename your folder first.">
+                                    <sanitizer sanitize="false"/>
+                                    <option value="(?P&lt;folderField1>.*)">field1</option>
+                                    <option value="(?P&lt;folderField1>.*)-(?P&lt;folderField2>[a-zA-Z0-9]+)">field1-field2</option>
+                                    <option value="(?P&lt;folderField1>.*)_(?P&lt;folderField2>[a-zA-Z0-9]+)">field1_field2</option>
+                                </param>
+                            </when>
+                        </conditional>
+                        <conditional name="con_metadata_extract_from">
+                            <param name="extract_metadata_from" type="select" label="Extract metadata from">
+                                <option value="All images">All images</option>
+                                <option value="Images matching a rule">Images matching a rule</option>
+                            </param>
+                            <when value="Images matching a rule">
+                                <expand macro="image_matching_rules_metadata" />
+                            </when>
+                            <when value="All images" />
+                        </conditional>
+                    </repeat>
+                </when>
+                <when value="No" />
+            </conditional>
+        </section>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/starting_modules_nameandtypes.xml	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,182 @@
+<macros>
+    <xml name="macro_image_type" token_thing="images">
+        <param name="name_to_assign" type="text" value="DNA" label="Name to assign these @THING@" />
+    </xml>
+    
+    <xml name="image_type_condition"> 
+        <conditional name="con_set_intensity">
+            <param name="set_intensity_range_from" type="select" label="Set intensity range from" help="This option determines how the image intensity should be rescaled from 0.0 - 1.0.">
+                <option value="Image metadata">Image metadata</option>
+                <option value="Image bit-depth">Image bit-depth</option>
+                <option value="Manual">Manual</option>
+            </param>
+            <when value="Manual">
+                <param name="maximum_intensity" type="float" value="255.0" label="Maximum intensity" help="The pixel value is divided, as read from the image file, by this value to get the loaded image’s per-pixel intensity." />
+
+            </when>
+            <when value="Image metadata" />
+            <when value="Image bit-depth" />
+        </conditional>
+    </xml>
+    <xml name="name_type_rule_matching_file">
+        <param name="operator" type="select">
+            <option value="does">Does</option>
+            <option value="doesnot">Does not</option>
+        </param>
+        <param name="contain" type="select">
+            <option value="contain">Contain</option>
+            <option value="Contain regular expression">Contain regular expression</option>
+            <option value="startwith">Start with</option>
+            <option value="endwith">End with</option>
+            <option value="Exactly match">Exactly match</option>
+        </param>
+        <param name="match_value" type="text"/>
+    </xml>
+    <xml name="name_type_rule_image">
+        <param name="operator" type="select">
+            <option value="does">Is</option>
+            <option value="doesnot">Is not</option>
+        </param>
+        <param name="match_type" type="select">
+            <option value="iscolor">Color</option>
+            <option value="ismonochrome">Monochrome</option>
+            <option value="isstack">Stack</option>
+            <option value="isstackframe">Stack frame</option>
+        </param>
+    </xml>
+    <xml name="name_type_rule_metadata">
+        <param name="operator" type="select">
+            <option value="does">Does</option>
+            <option value="doesnot">Does not</option>
+        </param>
+        <param name="match_type" type="select">
+            <option value="FileLocation">Have FileLocation matching</option>
+            <option value="Frame">Have Frame matching</option>
+            <option value="Screen">Have Screen matching</option>
+            <option value="Series">Have Series matching</option>
+        </param>
+        <param name="match_value" type="text"/>
+    </xml>
+    <xml name="name_type_rule_ext">
+        <param name="operator" type="select">
+            <option value="does">Is</option>
+            <option value="doesnot">Is not</option>
+        </param>
+        <param name="match_type" type="select">
+            <option value="istif">tif, tiff, ome.tif or ome.tiff</option>
+            <option value="isjpeg">jpg, jpeg</option>
+            <option value="ispng">png</option>
+            <option value="isimage">the extension of an image file</option>
+            <option value="isflex">flex</option>
+            <option value="ismovie">mov, avi</option>
+
+        </param>
+    </xml>
+    <xml name="image_matching_rules">
+        <repeat name="r_match_rule" title="Another image">
+            <param name="match_all_any" type="select" display="radio" label="Match the following rules">
+                <option value="and">All</option>
+                <option value="or">Any</option>
+            </param>
+            <repeat name="r_match" title="rule">
+                <conditional name="con_match">
+                    <param name="rule_type" type="select" label="Select rule criteria">
+                        <option value="file">File</option>
+                        <option value="directory">Directory</option>
+                        <option value="extension">Extension</option>
+                        <option value="image">Image</option>
+                        <option value="metadata">Metadata</option>
+                    </param>
+                    <when value="file">
+                        <expand macro="name_type_rule_matching_file"/>
+                    </when>
+                    <when value="directory">
+                        <expand macro="name_type_rule_matching_file"/>
+                    </when>
+                    <when value="extension">
+                        <expand macro="name_type_rule_ext" />
+                    </when>
+                    <when value="image">
+                        <expand macro="name_type_rule_image" />
+                    </when>
+                    <when value="metadata">
+                        <expand macro="name_type_rule_metadata" />
+                    </when>
+                </conditional>
+            </repeat>
+            <conditional name="con_select_image_type">
+                <param name="select_image_type" type="select" label="Select the image type" help="You can specify how these images should be treated">
+                    <option value="Grayscale image">Grayscale image</option>
+                    <option value="Color image">Color image</option>
+                    <option value="Binary mask">Binary mask</option>
+                    <option value="Illumination function">Illumination function</option>
+                    <option value="Objects">Objects</option>
+
+                </param>
+                <when value ="Grayscale image">
+                    <expand macro="macro_image_type" thing="images"/>
+                    <expand macro="image_type_condition" />
+                </when>
+                <when value="Color image">
+                    <expand macro="macro_image_type" thing="images"/>
+                    <expand macro="image_type_condition" />
+                </when>
+                <when value="Binary mask">
+                    <expand macro="macro_image_type" thing="images"/>
+                </when>
+                <when value="Illumination function">
+                    <expand macro="macro_image_type" thing="images"/>
+                </when>
+                <when value="Objects">
+                    <expand macro="macro_image_type" thing="objects"/>
+                </when>
+            </conditional>
+        </repeat>
+    </xml>
+    <xml name="starting_modules_nameandtypes">
+        <section name="nameandtypes" title="NamesAndTypes" expanded="false">
+            <conditional name="pixel_space">
+                <param name="process_3d" type="select" label="Process 3D" help="If you want to treat the data as three-dimensional, select 'Yes' to load files as volumes. Otherwise, select 'No' to load files as separate, two-dimensional images.">
+                    <option value="Yes">Yes, process 3D data</option>
+                    <option value="No">No, do not process 3D data</option>
+                </param>  
+                <when value="Yes">
+                    <param name="x_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the X dimension, relative to Y and Z" help="Normally, you will set one of these values to 1 and the others relative to that." />
+                    <param name="y_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the Y dimension, relative to X and Z"/>
+                    <param name="z_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the Z dimension, relative to X and Y"/>
+                </when>
+                <when value="No"/>
+            </conditional>
+            <conditional name="con_assign_a_name_to">
+                <param name="assign_a_name_to" type="select" label="Assign a name to" help="This setting allows you to specify a name for types of images or subsets of images so they can be treated separately by downstream tools.">
+                    <option value="All images">Give every image the same name</option>
+                    <option value="Images matching rules">Give images one of several names depending on the metadata</option>
+                </param>
+                <when value="All images">
+                    <expand macro="macro_image_type" thing="images" />
+                    <conditional name="con_select_image_type">
+                        <param name="select_image_type" type="select" label="Select the image type">
+                            <option value="Grayscale image">Grayscale image</option>
+                            <option value="Color image">Color image</option>
+                            <option value="Binary mask">Binary mask</option>
+                        </param>
+                        <when value ="Grayscale image">
+                            <expand macro="image_type_condition" />
+                        </when>
+                        <when value="Color image">
+                            <expand macro="image_type_condition" />
+                        </when>
+                        <when value="Binary mask" />
+                    </conditional>
+                </when>
+            <when value="Images matching rules">
+                <expand macro="image_matching_rules"/>
+                <param name="matching_method" type="select" label="Image set matching method">
+                    <option value="Order">Order</option>
+                    <option value="Metadata">Metadata</option>
+                </param>
+            </when>
+        </conditional>
+    </section>
+</xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ExampleHuman.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,246 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:300
+GitHash:
+ModuleCount:14
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot containregexp "\x5B\\\\\\\\\\\\\\\\/\x5D\\\\\\\\.")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:No
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)_w(?P<ChannelNumber>\x5B0-9\x5D)
+    Regular expression to extract from folder name:(?P<Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:\x5B\x5D
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'DNA\x3A DNA stained with DAPI\', \'PH3\x3A An antibody for phosphorylated histone H3 correlated with mitosis\', \'cellbody\x3A \'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:\x5B\x5D
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:3
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does contain "d0.tif")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+    Select the rule criteria:and (file does contain "d1.tif")
+    Name to assign these images:PH3
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+    Select the rule criteria:and (file does contain "d2.tif")
+    Name to assign these images:cellbody
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:No
+    grouping metadata count:1
+    Metadata category:None
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):8,80
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Intensity
+    Method to draw dividing lines between clumped objects:Intensity
+    Size of smoothing filter:10
+    Suppress local maxima that are closer than this minimum allowed distance:7.0
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After declumping only
+    Automatically calculate size of smoothing filter for declumping?:Yes
+    Automatically calculate minimum allowed distance between local maxima?:Yes
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:No
+    Threshold setting version:10
+    Threshold strategy:Global
+    Thresholding method:Minimum cross entropy
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0.0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.0
+    Thresholding method:Otsu
+
+IdentifyPrimaryObjects:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:PH3
+    Name the primary objects to be identified:PH3
+    Typical diameter of objects, in pixel units (Min,Max):8,80
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Intensity
+    Method to draw dividing lines between clumped objects:Intensity
+    Size of smoothing filter:10
+    Suppress local maxima that are closer than this minimum allowed distance:7.0
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After declumping only
+    Automatically calculate size of smoothing filter for declumping?:Yes
+    Automatically calculate minimum allowed distance between local maxima?:Yes
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:No
+    Threshold setting version:10
+    Threshold strategy:Global
+    Thresholding method:Minimum cross entropy
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0.0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.0
+    Thresholding method:Otsu
+
+RelateObjects:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Parent objects:Nuclei
+    Child objects:PH3
+    Calculate child-parent distances?:None
+    Calculate per-parent means for all child measurements?:No
+    Calculate distances to other parents?:No
+    Parent name:None
+
+IdentifySecondaryObjects:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:10|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input objects:Nuclei
+    Name the objects to be identified:Cells
+    Select the method to identify the secondary objects:Propagation
+    Select the input image:cellbody
+    Number of pixels by which to expand the primary objects:10
+    Regularization factor:0.05
+    Discard secondary objects touching the border of the image?:No
+    Discard the associated primary objects?:No
+    Name the new primary objects:FilteredNuclei
+    Fill holes in identified objects?:Yes
+    Threshold setting version:10
+    Threshold strategy:Global
+    Thresholding method:Otsu
+    Threshold smoothing scale:0.0
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0.0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Three classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.0
+    Thresholding method:Otsu
+
+IdentifyTertiaryObjects:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the larger identified objects:Cells
+    Select the smaller identified objects:Nuclei
+    Name the tertiary objects to be identified:Cytoplasm
+    Shrink smaller object prior to subtraction?:Yes
+
+MeasureObjectIntensity:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Hidden:2
+    Select an image to measure:DNA
+    Select an image to measure:PH3
+    Select objects to measure:Nuclei
+    Select objects to measure:Cells
+    Select objects to measure:Cytoplasm
+
+MeasureObjectSizeShape:[module_num:11|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select objects to measure:Nuclei
+    Select objects to measure:Cells
+    Select objects to measure:Cytoplasm
+    Calculate the Zernike features?:Yes
+
+OverlayOutlines:[module_num:12|svn_version:\'Unknown\'|variable_revision_number:4|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Display outlines on a blank image?:No
+    Select image on which to display outlines:DNA
+    Name the output image:OrigOverlay
+    Outline display mode:Color
+    Select method to determine brightness of outlines:Max of image
+    How to outline:Thick
+    Select outline color:#0080FF
+    Select objects to display:Cells
+    Select outline color:blue
+    Select objects to display:Nuclei
+    Select outline color:yellow
+    Select objects to display:PH3
+
+SaveImages:[module_num:13|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the type of image to save:Image
+    Select the image to save:OrigOverlay
+    Select method for constructing file names:From image filename
+    Select image name for file prefix:DNA
+    Enter single file name:OrigBlue
+    Number of digits:4
+    Append a suffix to the image file name?:Yes
+    Text to append to the image name:_Overlay
+    Saved file format:png
+    Output file location:Default Output Folder\x7C
+    Image bit depth:8-bit integer
+    Overwrite existing files without warning?:Yes
+    When to save:Every cycle
+    Record the file and path information to the saved image?:Yes
+    Create subfolders in the output folder?:No
+    Base image folder:Elsewhere...\x7C
+
+ExportToSpreadsheet:[module_num:14|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the column delimiter:Comma (",")
+    Add image metadata columns to your object data file?:No
+    Select the measurements to export:No
+    Calculate the per-image mean values for object measurements?:No
+    Calculate the per-image median values for object measurements?:No
+    Calculate the per-image standard deviation values for object measurements?:No
+    Output file location:Default Output Folder\x7C
+    Create a GenePattern GCT file?:No
+    Select source of sample row name:Metadata
+    Select the image to use as the identifier:None
+    Select the metadata to use as the identifier:None
+    Export all measurement types?:Yes
+    Press button to select measurements:
+    Representation of Nan/Inf:NaN
+    Add a prefix to file names?:No
+    Filename prefix:MyExpt_
+    Overwrite existing files without warning?:Yes
+    Data to export:Do not use
+    Combine these object measurements with those of the previous object?:No
+    File name:DATA.csv
+    Use the object name for the file name?:Yes
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/color_to_gray.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,79 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ColorToGray:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:True|notes:\x5B\'Convert the color image to grayscale.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:OrigColor
+    Conversion method:Combine
+    Image type:RGB
+    Name the output image:OrigGray
+    Relative weight of the red channel:1.0
+    Relative weight of the green channel:1.0
+    Relative weight of the blue channel:1.0
+    Convert red to gray?:Yes
+    Name the output image:OrigRed
+    Convert green to gray?:Yes
+    Name the output image:OrigGreen
+    Convert blue to gray?:Yes
+    Name the output image:OrigBlue
+    Convert hue to gray?:Yes
+    Name the output image:OrigHue
+    Convert saturation to gray?:Yes
+    Name the output image:OrigSaturation
+    Convert value to gray?:Yes
+    Name the output image:OrigValue
+    Channel count:1
+    Channel number:Red\x3A 1
+    Relative weight of the channel:1.0
+    Image name:Channel1
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/color_to_gray_combine_channels.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,82 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ColorToGray:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:True|notes:\x5B\'Convert the color image to grayscale.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Conversion method:Combine
+    Image type:Channels
+    Name the output image:OrigGray
+    Relative weight of the red channel:1.0
+    Relative weight of the green channel:1.0
+    Relative weight of the blue channel:1.0
+    Convert red to gray?:Yes
+    Name the output image:OrigRed
+    Convert green to gray?:Yes
+    Name the output image:OrigGreen
+    Convert blue to gray?:Yes
+    Name the output image:OrigBlue
+    Convert hue to gray?:Yes
+    Name the output image:OrigHue
+    Convert saturation to gray?:Yes
+    Name the output image:OrigSaturation
+    Convert value to gray?:Yes
+    Name the output image:OrigValue
+    Channel count:2
+    Channel number:2
+    Relative weight of the channel:0.2
+    Image name:Channel1
+    Channel number:3
+    Relative weight of the channel:0.5
+    Image name:Channel1
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/color_to_gray_split_channels.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,82 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ColorToGray:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:True|notes:\x5B\'Convert the color image to grayscale.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Conversion method:Split
+    Image type:Channels
+    Name the output image:OrigGray
+    Relative weight of the red channel:1.0
+    Relative weight of the green channel:1.0
+    Relative weight of the blue channel:1.0
+    Convert red to gray?:Yes
+    Name the output image:OrigRed
+    Convert green to gray?:Yes
+    Name the output image:OrigGreen
+    Convert blue to gray?:Yes
+    Name the output image:OrigBlue
+    Convert hue to gray?:Yes
+    Name the output image:OrigHue
+    Convert saturation to gray?:Yes
+    Name the output image:OrigSaturation
+    Convert value to gray?:Yes
+    Name the output image:OrigValue
+    Channel count:2
+    Channel number:2
+    Relative weight of the channel:1.0
+    Image name:Image2
+    Channel number:3
+    Relative weight of the channel:1.0
+    Image name:Image3
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/color_to_gray_split_hsv.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,79 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ColorToGray:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:True|notes:\x5B\'Convert the color image to grayscale.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Conversion method:Split
+    Image type:HSV
+    Name the output image:OrigGray
+    Relative weight of the red channel:1.0
+    Relative weight of the green channel:1.0
+    Relative weight of the blue channel:1.0
+    Convert red to gray?:Yes
+    Name the output image:OrigRed
+    Convert green to gray?:Yes
+    Name the output image:OrigGreen
+    Convert blue to gray?:Yes
+    Name the output image:OrigBlue
+    Convert hue to gray?:Yes
+    Name the output image:OutputHue
+    Convert saturation to gray?:No
+    Name the output image:
+    Convert value to gray?:Yes
+    Name the output image:OutputValue
+    Channel count:1
+    Channel number:Red\x3A 1
+    Relative weight of the channel:1.0
+    Image name:Channel1
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/color_to_gray_split_rgb.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,79 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ColorToGray:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:True|notes:\x5B\'Convert the color image to grayscale.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Conversion method:Split
+    Image type:RGB
+    Name the output image:OrigGray
+    Relative weight of the red channel:1.0
+    Relative weight of the green channel:1.0
+    Relative weight of the blue channel:1.0
+    Convert red to gray?:Yes
+    Name the output image:OutputRed
+    Convert green to gray?:Yes
+    Name the output image:OutputGreen
+    Convert blue to gray?:No
+    Name the output image:
+    Convert hue to gray?:Yes
+    Name the output image:OrigHue
+    Convert saturation to gray?:Yes
+    Name the output image:OrigSaturation
+    Convert value to gray?:Yes
+    Name the output image:OrigValue
+    Channel count:1
+    Channel number:Red\x3A 1
+    Relative weight of the channel:1.0
+    Image name:Channel1
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/common-complicated.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,73 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:4
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:2
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:Images matching a rule
+    Select the filtering criteria:and (file does contain "im") (extension does istif)
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:Folder name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)_(?P<folderField2>[a-zA-Z0-9]+)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:3
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does contain "im") (image doesnot ismonochrome)
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Objects
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+    Select the rule criteria:and (file does contain "")
+    Name to assign these images:GFP
+    Name to assign these objects:Cell
+    Select the image type:Illumination function
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+    Select the rule criteria:or (extension does istif)
+    Name to assign these images:Actin
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/common-nogroup.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,73 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:4
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:2
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:Images matching a rule
+    Select the filtering criteria:and (file does contain "im") (extension does istif)
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:Folder name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)_(?P<folderField2>[a-zA-Z0-9]+)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:3
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does contain "im") (image doesnot ismonochrome)
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Objects
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+    Select the rule criteria:and (file does contain "")
+    Name to assign these images:GFP
+    Name to assign these objects:Cell
+    Select the image type:Illumination function
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+    Select the rule criteria:or (extension does istif)
+    Name to assign these images:Actin
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:No
+    grouping metadata count:1
+    Metadata category:None
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/common.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,53 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:4
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/common_image_math.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,94 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:6
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<field1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:Screen
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nucleus
+    Typical diameter of objects, in pixel units (Min,Max):15,200
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Intensity
+    Method to draw dividing lines between clumped objects:Intensity
+    Size of smoothing filter:10
+    Suppress local maxima that are closer than this minimum allowed distance:7.0
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:Yes
+    Automatically calculate minimum allowed distance between local maxima?:Yes
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:No
+    Threshold setting version:10
+    Threshold strategy:Global
+    Thresholding method:Minimum cross entropy
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0.0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.0
+    Thresholding method:Otsu
+
+ConvertObjectsToImage:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input objects:Nucleus
+    Name the output image:CellImage
+    Select the color format:Binary (black & white)
+    Select the colormap:Default
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/convert_objects_to_image.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,59 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ConvertObjectsToImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input objects:Nuclei
+    Name the output image:MaskNuclei
+    Select the color format:Binary (black & white)
+    Select the colormap:Default
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/display_data_on_image.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,70 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+DisplayDataOnImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\'Add nuclei id as label\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Display object or image measurements?:Object
+    Select the input objects:Nuclei
+    Measurement to display:Number_Object_Number
+    Select the image on which to display the measurements:DNA
+    Text color:#ff0000
+    Name the output image that has the measurements displayed:ImageDisplay
+    Font size (points):11
+    Number of decimals:0
+    Image elements to save:Image
+    Annotation offset (in pixels):0
+    Display mode:Text
+    Color map:Default
+    Display background image?:Yes
+    Color map scale:Use this image's measurement range
+    Color map range:0.0,1.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/enhance_or_suppress_features.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,66 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+EnhanceOrSuppressFeatures:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\'Identify nucleoli\', \'PARAMS\x3A Range of hole sizes'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the output image:DNAdarkholes
+    Select the operation:Enhance
+    Feature size:10
+    Feature type:Dark holes
+    Range of hole sizes:1,15
+    Smoothing scale:2.0
+    Shear angle:0.0
+    Decay:0.95
+    Enhancement method:Tubeness
+    Speed and accuracy:Fast
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_to_spreadsheet.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,76 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ExportToSpreadsheet:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the column delimiter:Tab
+    Add image metadata columns to your object data file?:Yes
+    Select the measurements to export:No
+    Calculate the per-image mean values for object measurements?:Yes
+    Calculate the per-image median values for object measurements?:Yes
+    Calculate the per-image standard deviation values for object measurements?:Yes
+    Output file location:Default Output Folder\x7C
+    Create a GenePattern GCT file?:No
+    Select source of sample row name:Metadata
+    Select the image to use as the identifier:None
+    Select the metadata to use as the identifier:None
+    Export all measurement types?:Yes
+    Press button to select measurements:
+    Representation of Nan/Inf:NaN
+    Add a prefix to file names?:No
+    Filename prefix:MyPrefix_
+    Overwrite existing files without warning?:Yes
+    Data to export:Do not use
+    Combine these object measurements with those of the previous object?:No
+    File name:DATA.csv
+    Use the object name for the file name?:Yes
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_to_spreadsheet_create_gene_image_filename.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,76 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ExportToSpreadsheet:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the column delimiter:Tab
+    Add image metadata columns to your object data file?:Yes
+    Select the measurements to export:No
+    Calculate the per-image mean values for object measurements?:Yes
+    Calculate the per-image median values for object measurements?:Yes
+    Calculate the per-image standard deviation values for object measurements?:Yes
+    Output file location:Default Output Folder\x7C
+    Create a GenePattern GCT file?:Yes
+    Select source of sample row name:Image filename
+    Select the image to use as the identifier:DNA
+    Select the metadata to use as the identifier:None
+    Export all measurement types?:No
+    Press button to select measurements:
+    Representation of Nan/Inf:NaN
+    Add a prefix to file names?:Yes
+    Filename prefix:MyExpt_
+    Overwrite existing files without warning?:Yes
+    Data to export:Image
+    Combine these object measurements with those of the previous object?:No
+    File name:data.csv
+    Use the object name for the file name?:No
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_to_spreadsheet_create_gene_metadata.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,76 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ExportToSpreadsheet:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the column delimiter:Tab
+    Add image metadata columns to your object data file?:Yes
+    Select the measurements to export:No
+    Calculate the per-image mean values for object measurements?:Yes
+    Calculate the per-image median values for object measurements?:Yes
+    Calculate the per-image standard deviation values for object measurements?:Yes
+    Output file location:Default Output Folder\x7C
+    Create a GenePattern GCT file?:Yes
+    Select source of sample row name:Metadata
+    Select the image to use as the identifier:None
+    Select the metadata to use as the identifier:FileName_DNA
+    Export all measurement types?:Yes
+    Press button to select measurements:
+    Representation of Nan/Inf:NaN
+    Add a prefix to file names?:No
+    Filename prefix:MyPrefix_
+    Overwrite existing files without warning?:Yes
+    Data to export:Do not use
+    Combine these object measurements with those of the previous object?:No
+    File name:DATA.csv
+    Use the object name for the file name?:Yes
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_to_spreadsheet_multi.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,80 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ExportToSpreadsheet:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the column delimiter:Tab
+    Add image metadata columns to your object data file?:Yes
+    Select the measurements to export:No
+    Calculate the per-image mean values for object measurements?:Yes
+    Calculate the per-image median values for object measurements?:Yes
+    Calculate the per-image standard deviation values for object measurements?:Yes
+    Output file location:Default Output Folder\x7C
+    Create a GenePattern GCT file?:Yes
+    Select source of sample row name:Image filename
+    Select the image to use as the identifier:DNA
+    Select the metadata to use as the identifier:None
+    Export all measurement types?:No
+    Press button to select measurements:
+    Representation of Nan/Inf:NaN
+    Add a prefix to file names?:Yes
+    Filename prefix:MyExpt_
+    Overwrite existing files without warning?:Yes
+    Data to export:Image
+    Combine these object measurements with those of the previous object?:No
+    File name:data.csv
+    Use the object name for the file name?:No
+    Data to export:Experiment
+    Combine these object measurements with those of the previous object?:No
+    File name:DATA.csv
+    Use the object name for the file name?:Yes
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gray_to_color.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,75 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+GrayToColor:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\'Combine masks nuclei + nucleoli with colors\'\x5D|batch_state:array(\x5B], dtype=uint8)|enabled:True|wants_pause:False]
+    Select a color scheme:RGB
+    Select the image to be colored red:MaskNucleoli
+    Select the image to be colored green:Leave this black
+    Select the image to be colored blue:MaskNuclei
+    Name the output image:CombinedMask
+    Relative weight for the red image:0.8
+    Relative weight for the green image:1.0
+    Relative weight for the blue image:0.5
+    Select the image to be colored cyan:Leave this black
+    Select the image to be colored magenta:Leave this black
+    Select the image to be colored yellow:Leave this black
+    Select the image that determines brightness:Leave this black
+    Relative weight for the cyan image:1.0
+    Relative weight for the magenta image:1.0
+    Relative weight for the yellow image:1.0
+    Relative weight for the brightness image:1.0
+    Hidden:1
+    Image name:None
+    Color:#FF0000
+    Weight:1.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\'Identify the nuclei from the DNA channel.\', \'PARAMS\x3A\', \'- Typical diameter of objects (Min,Max)\', \'- Method to distinguish clumped objects\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):15,200
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Shape
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:0
+    Suppress local maxima that are closer than this minimum allowed distance:7
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:Yes
+    Automatically calculate minimum allowed distance between local maxima?:Yes
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:Otsu
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:0.9
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:500
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.0
+    Thresholding method:Otsu
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_adv_adaptive_otsu.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\'Identify the nuclei from the DNA channel.\', \'PARAMS\x3A\', \'- Typical diameter of objects (Min,Max)\', \'- Method to distinguish clumped objects\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):15,200
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Shape
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:1
+    Suppress local maxima that are closer than this minimum allowed distance:1
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:No
+    Automatically calculate minimum allowed distance between local maxima?:No
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Adaptive
+    Thresholding method:Otsu
+    Threshold smoothing scale:1.5000
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Three classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.00
+    Thresholding method:Otsu
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_adv_global_manual.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\'Identify the nuclei from the DNA channel.\', \'PARAMS\x3A\', \'- Typical diameter of objects (Min,Max)\', \'- Method to distinguish clumped objects\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):5,20
+    Discard objects outside the diameter range?:No
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Shape
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:1
+    Suppress local maxima that are closer than this minimum allowed distance:1
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:No
+    Automatically calculate minimum allowed distance between local maxima?:No
+    Handling of objects if excessive number of objects identified:Erase
+    Maximum number of objects:499
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:Manual
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:1
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.00
+    Thresholding method:Manual
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_adv_global_mce.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\'Identify the nuclei from the DNA channel.\', \'PARAMS\x3A\', \'- Typical diameter of objects (Min,Max)\', \'- Method to distinguish clumped objects\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):15,40
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Shape
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:1
+    Suppress local maxima that are closer than this minimum allowed distance:7
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:No
+    Automatically calculate minimum allowed distance between local maxima?:No
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:Minimum cross entropy
+    Threshold smoothing scale:1.5000
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.00
+    Thresholding method:Minimum cross entropy
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_adv_global_measurement.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\'Identify the nuclei from the DNA channel.\', \'PARAMS\x3A\', \'- Typical diameter of objects (Min,Max)\', \'- Method to distinguish clumped objects\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):5,20
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:No
+    Method to distinguish clumped objects:Intensity
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:0
+    Suppress local maxima that are closer than this minimum allowed distance:6
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:Yes
+    Automatically calculate minimum allowed distance between local maxima?:No
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:Measurement
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.1,0.4
+    Manual threshold:0
+    Select the measurement to threshold with:FileName_DNA
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.00
+    Thresholding method:Measurement
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_adv_global_rb.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\'Identify the nuclei from the DNA channel.\', \'PARAMS\x3A\', \'- Typical diameter of objects (Min,Max)\', \'- Method to distinguish clumped objects\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):10,40
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Shape
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:1
+    Suppress local maxima that are closer than this minimum allowed distance:7
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:No
+    Automatically calculate minimum allowed distance between local maxima?:No
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:RobustBackground
+    Threshold smoothing scale:1.4000
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.06
+    Upper outlier fraction:0.07
+    Averaging method:Median
+    Variance method:Median absolute deviation
+    # of deviations:3.00
+    Thresholding method:RobustBackground
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_noadv.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\'Identify the nuclei from the DNA channel.\', \'PARAMS\x3A\', \'- Typical diameter of objects (Min,Max)\', \'- Method to distinguish clumped objects\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):15,200
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Intensity
+    Method to draw dividing lines between clumped objects:Intensity
+    Size of smoothing filter:1
+    Suppress local maxima that are closer than this minimum allowed distance:7
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:Yes
+    Automatically calculate minimum allowed distance between local maxima?:Yes
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:No
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:Minimum cross entropy
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.00
+    Thresholding method:Minimum cross entropy
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/image_math_1.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,112 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:7
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<field1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:Screen
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nucleus
+    Typical diameter of objects, in pixel units (Min,Max):15,200
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Intensity
+    Method to draw dividing lines between clumped objects:Intensity
+    Size of smoothing filter:10
+    Suppress local maxima that are closer than this minimum allowed distance:7.0
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:Yes
+    Automatically calculate minimum allowed distance between local maxima?:Yes
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:No
+    Threshold setting version:10
+    Threshold strategy:Global
+    Thresholding method:Minimum cross entropy
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0.0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.0
+    Thresholding method:Otsu
+
+ConvertObjectsToImage:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input objects:Nucleus
+    Name the output image:CellImage
+    Select the color format:Binary (black & white)
+    Select the colormap:Default
+
+ImageMath:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Operation:Add
+    Raise the power of the result by:1.0
+    Multiply the result by:1.0
+    Add to result:0.0
+    Set values less than 0 equal to 0?:Yes
+    Set values greater than 1 equal to 1?:Yes
+    Ignore the image masks?:No
+    Name the output image:ImageAfterMath
+    Image or measurement?:Image
+    Select the first image:DNA
+    Multiply the first image by:1.0
+    Measurement:
+    Image or measurement?:Image
+    Select the second image:CellImage
+    Multiply the second image by:2.0
+    Measurement:
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/image_math_2.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,112 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:7
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<field1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:Screen
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nucleus
+    Typical diameter of objects, in pixel units (Min,Max):15,200
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Intensity
+    Method to draw dividing lines between clumped objects:Intensity
+    Size of smoothing filter:10
+    Suppress local maxima that are closer than this minimum allowed distance:7.0
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:Yes
+    Automatically calculate minimum allowed distance between local maxima?:Yes
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:No
+    Threshold setting version:10
+    Threshold strategy:Global
+    Thresholding method:Minimum cross entropy
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0.0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.0
+    Thresholding method:Otsu
+
+ConvertObjectsToImage:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input objects:Nucleus
+    Name the output image:CellImage
+    Select the color format:Binary (black & white)
+    Select the colormap:Default
+
+ImageMath:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Operation:Subtract
+    Raise the power of the result by:1.0
+    Multiply the result by:1.0
+    Add to result:0.0
+    Set values less than 0 equal to 0?:Yes
+    Set values greater than 1 equal to 1?:No
+    Ignore the image masks?:No
+    Name the output image:ImageAfterMath
+    Image or measurement?:Image
+    Select the first image:DNA
+    Multiply the first image by:1.0
+    Measurement:
+    Image or measurement?:Measurement
+    Select the second image:
+    Multiply the second image by:5.0
+    Measurement:FileName_DNA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/image_math_3.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,112 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:7
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<field1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:Screen
+
+IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nucleus
+    Typical diameter of objects, in pixel units (Min,Max):15,200
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Intensity
+    Method to draw dividing lines between clumped objects:Intensity
+    Size of smoothing filter:10
+    Suppress local maxima that are closer than this minimum allowed distance:7.0
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:Yes
+    Automatically calculate minimum allowed distance between local maxima?:Yes
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:No
+    Threshold setting version:10
+    Threshold strategy:Global
+    Thresholding method:Minimum cross entropy
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0.0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.0
+    Thresholding method:Otsu
+
+ConvertObjectsToImage:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input objects:Nucleus
+    Name the output image:CellImage
+    Select the color format:Binary (black & white)
+    Select the colormap:Default
+
+ImageMath:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Operation:Not
+    Raise the power of the result by:
+    Multiply the result by:
+    Add to result:
+    Set values less than 0 equal to 0?:
+    Set values greater than 1 equal to 1?:
+    Ignore the image masks?:No
+    Name the output image:ImageAfterMath
+    Image or measurement?:Image
+    Select the first image:DNA
+    Multiply the first image by:
+    Measurement:
+    Image or measurement?:
+    Select the second image:
+    Multiply the second image by:
+    Measurement:
Binary file test-data/images.tar has changed
Binary file test-data/images/AS_09125_050116030001_D03f00d0.tif has changed
Binary file test-data/images/AS_09125_050116030001_D03f00d1.tif has changed
Binary file test-data/images/AS_09125_050116030001_D03f00d2.tif has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mask_image.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,61 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MaskImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B'Keep only nucleoli inside the nuclei\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNAdarkholes
+    Name the output image:MaskDNAdarkholes
+    Use objects or an image as a mask?:Objects
+    Select object for mask:Nuclei
+    Select image for mask:None
+    Invert the mask?:No
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_granularity.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,62 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureGranularity:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\'PARAMS\x3A\', \'- Radius\', '- Range\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Image count:1
+    Object count:0
+    Select an image to measure:DNA
+    Subsampling factor for granularity measurements:0.25
+    Subsampling factor for background reduction:0.25
+    Radius of structuring element:10
+    Range of the granular spectrum:16
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_image_area_occupied.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,62 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureImageAreaOccupied:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Hidden:2
+    Measure the area occupied in a binary image, or in objects?:Objects
+    Select objects to measure:Nuclei
+    Select a binary image to measure:None
+    Measure the area occupied in a binary image, or in objects?:Objects
+    Select objects to measure:Nucleoli
+    Select a binary image to measure:None
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_image_intensity.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,61 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureImageIntensity:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the image to measure:DNA
+    Measure the intensity only from areas enclosed by objects?:No
+    Select the input objects:None
+    Select the image to measure:DNA
+    Measure the intensity only from areas enclosed by objects?:Yes
+    Select the input objects:Nuclei
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_image_quality.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,72 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureImageQuality:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Calculate metrics for which images?:All loaded images
+    Image count:1
+    Scale count:1
+    Threshold count:1
+    Select the images to measure:
+    Include the image rescaling value?:Yes
+    Calculate blur metrics?:Yes
+    Spatial scale for blur measurements:20
+    Calculate saturation metrics?:Yes
+    Calculate intensity metrics?:Yes
+    Calculate thresholds?:Yes
+    Use all thresholding methods?:No
+    Select a thresholding method:Otsu
+    Typical fraction of the image covered by objects:0.1
+    Two-class or three-class thresholding?:Two classes
+    Minimize the weighted variance or the entropy:Weighted variance
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_object_intensity.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,58 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureObjectIntensity:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Hidden:1
+    Select an image to measure:DNA
+    Select objects to measure:Nuclei
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_object_size_shape.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,58 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureObjectSizeShape:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select objects to measure:Nuclei
+    Select objects to measure:Nucleoli
+    Calculate the Zernike features?:Yes
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_texture.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,62 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureTexture:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\'PARAMS\x3A\', \'- Texture scale']|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Hidden:1
+    Hidden:1
+    Hidden:1
+    Select an image to measure:DNA
+    Select objects to measure:Nuclei
+    Texture scale to measure:3
+    Measure images or objects?:Objects
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/overlay_outlines.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,63 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+OverlayOutlines:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:True|notes:\x5B\'Overlay the embryo outlines on the grayscale image.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Display outlines on a blank image?:No
+    Select image on which to display outlines:OrigGray
+    Name the output image:OutlineImage
+    Outline display mode:Color
+    Select method to determine brightness of outlines:Max of image
+    How to outline:Inner
+    Select outline color:#FF0000
+    Select objects to display:Embryos
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/overlay_outlines_blank_color.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,65 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+OverlayOutlines:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:True|notes:\x5B\'Overlay the embryo outlines on the grayscale image.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Display outlines on a blank image?:Yes
+    Select image on which to display outlines:None
+    Name the output image:OutputImage
+    Outline display mode:Color
+    Select method to determine brightness of outlines:Max of image
+    How to outline:Inner
+    Select outline color:#548dd4
+    Select objects to display:DNA1
+    Select outline color:#000000
+    Select objects to display:DNA3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/overlay_outlines_blank_grayscale.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,65 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+OverlayOutlines:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:True|notes:\x5B\'Overlay the embryo outlines on the grayscale image.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Display outlines on a blank image?:Yes
+    Select image on which to display outlines:None
+    Name the output image:OutputImage
+    Outline display mode:Grayscale
+    Select method to determine brightness of outlines:Max of image
+    How to outline:Outer
+    Select outline color:#FF0000
+    Select objects to display:DNA
+    Select outline color:#FF0000
+    Select objects to display:DNA1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/overlay_outlines_non_blank_color.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,63 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+OverlayOutlines:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:True|notes:\x5B\'Overlay the embryo outlines on the grayscale image.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Display outlines on a blank image?:No
+    Select image on which to display outlines:OrigGray
+    Name the output image:OutlineImage
+    Outline display mode:Color
+    Select method to determine brightness of outlines:Max of image
+    How to outline:Inner
+    Select outline color:#FF0000
+    Select objects to display:Embryos
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/overlay_outlines_non_blank_grayscale.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,65 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+OverlayOutlines:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:True|notes:\x5B\'Overlay the embryo outlines on the grayscale image.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Display outlines on a blank image?:No
+    Select image on which to display outlines:DNA1
+    Name the output image:OutputImage
+    Outline display mode:Grayscale
+    Select method to determine brightness of outlines:Max possible
+    How to outline:Thick
+    Select outline color:#FF0000
+    Select objects to display:Object1
+    Select outline color:#FF0000
+    Select objects to display:Object2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/relate_objects.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,62 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+RelateObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Parent objects:Nuclei
+    Child objects:Nucleoli
+    Calculate child-parent distances?:Both
+    Calculate per-parent means for all child measurements?:Yes
+    Calculate distances to other parents?:No
+    Do you want to save the children with parents as a new object set?:Yes
+    Name the output object:RelateObjects
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/save_images.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,71 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+SaveImages:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the type of image to save:Image
+    Select the image to save:ImageDisplay
+    Select method for constructing file names:From image filename
+    Select image name for file prefix:DNA
+    Enter single file name:OrigBlue
+    Number of digits:4
+    Append a suffix to the image file name?:Yes
+    Text to append to the image name:_nucleiNumbers
+    Saved file format:tiff
+    Output file location:Default Output Folder\x7Coutput
+    Image bit depth:8-bit integer
+    Overwrite existing files without warning?:Yes
+    When to save:Every cycle
+    Record the file and path information to the saved image?:No
+    Create subfolders in the output folder?:No
+    Base image folder:Elsewhere...
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tile.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,68 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+Tile:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\'Tile the original color image, the outlined image and the image of tracked labels together.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select an input image:OrigColor
+    Name the output image:AdjacentImage
+    Tile assembly method:Within cycles
+    Final number of rows:1
+    Final number of columns:12
+    Image corner to begin tiling:top left
+    Direction to begin tiling:row
+    Use meander mode?:No
+    Automatically calculate number of rows?:No
+    Automatically calculate number of columns?:Yes
+    Select an additional image to tile:OutlineImage
+    Select an additional image to tile:TrackedCells
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tile_across_cycles.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,66 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+Tile:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\'Tile the original color image, the outlined image and the image of tracked labels together.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select an input image:DNA
+    Name the output image:TiledImage
+    Tile assembly method:Across cycles
+    Final number of rows:8
+    Final number of columns:5
+    Image corner to begin tiling:top right
+    Direction to begin tiling:column
+    Use meander mode?:No
+    Automatically calculate number of rows?:Yes
+    Automatically calculate number of columns?:No
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tile_across_cyles.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,65 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+Tile:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\'Tile the original color image, the outlined image and the image of tracked labels together.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select an input image:DNA
+    Name the output image:TiledImage
+    Tile assembly method:Across cycles
+    Final number of rows:8
+    Final number of columns:5
+    Image corner to begin tiling:top right
+    Direction to begin tiling:column
+    Use meander mode?:No
+    Automatically calculate number of rows?:Yes
+    Automatically calculate number of columns?:No
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/track_object.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,85 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+TrackObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\'Track the embryos across images using the Overlap method\x3A tracked objects are identified by the amount of frame-to-frame overlap. Save an image of embryos labeled with a unique number across time.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Choose a tracking method:Overlap
+    Select the objects to track:Embryos
+    Select object measurement to use for tracking:None
+    Maximum pixel distance to consider matches:50
+    Select display option:Color and Number
+    Save color-coded image?:Yes
+    Name the output image:TrackedCells
+    Select the movement model:Both
+    Number of standard deviations for search radius:3.0
+    Search radius limit, in pixel units (Min,Max):2.0,10.0
+    Run the second phase of the LAP algorithm?:Yes
+    Gap closing cost:40
+    Split alternative cost:40
+    Merge alternative cost:40
+    Maximum gap displacement, in pixel units:5
+    Maximum split score:50
+    Maximum merge score:50
+    Maximum temporal gap, in frames:5
+    Filter objects by lifetime?:No
+    Filter using a minimum lifetime?:Yes
+    Minimum lifetime:1
+    Filter using a maximum lifetime?:No
+    Maximum lifetime:100
+    Mitosis alternative cost:80
+    Maximum mitosis distance, in pixel units:40
+    Average cell diameter in pixels:35.0
+    Use advanced configuration parameters:No
+    Cost of cell to empty matching:15.0
+    Weight of area difference in function matching cost:25.0
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/track_object_distance_no_filter_min.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,85 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+TrackObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\'Track the embryos across images using the Overlap method\x3A tracked objects are identified by the amount of frame-to-frame overlap. Save an image of embryos labeled with a unique number across time.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Choose a tracking method:Distance
+    Select the objects to track:DNA
+    Select object measurement to use for tracking:None
+    Maximum pixel distance to consider matches:50
+    Select display option:Color and Number
+    Save color-coded image?:Yes
+    Name the output image:OutputImage
+    Select the movement model:Both
+    Number of standard deviations for search radius:3.0
+    Search radius limit, in pixel units (Min,Max):2.0,10.0
+    Run the second phase of the LAP algorithm?:Yes
+    Gap closing cost:40
+    Split alternative cost:40
+    Merge alternative cost:40
+    Maximum gap displacement, in pixel units:5
+    Maximum split score:50
+    Maximum merge score:50
+    Maximum temporal gap, in frames:5
+    Filter objects by lifetime?:Yes
+    Filter using a minimum lifetime?:No
+    Minimum lifetime:1
+    Filter using a maximum lifetime?:Yes
+    Maximum lifetime:80
+    Mitosis alternative cost:80
+    Maximum mitosis distance, in pixel units:40
+    Average cell diameter in pixels:35.0
+    Use advanced configuration parameters:No
+    Cost of cell to empty matching:15.0
+    Weight of area difference in function matching cost:25.0
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/track_object_follow_neighbors.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,85 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+TrackObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\'Track the embryos across images using the Overlap method\x3A tracked objects are identified by the amount of frame-to-frame overlap. Save an image of embryos labeled with a unique number across time.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Choose a tracking method:Follow Neighbors
+    Select the objects to track:DNA
+    Select object measurement to use for tracking:None
+    Maximum pixel distance to consider matches:60
+    Select display option:Color only
+    Save color-coded image?:Yes
+    Name the output image:OutputImage
+    Select the movement model:Both
+    Number of standard deviations for search radius:3.0
+    Search radius limit, in pixel units (Min,Max):2.0,10.0
+    Run the second phase of the LAP algorithm?:Yes
+    Gap closing cost:40
+    Split alternative cost:40
+    Merge alternative cost:40
+    Maximum gap displacement, in pixel units:5
+    Maximum split score:50
+    Maximum merge score:50
+    Maximum temporal gap, in frames:5
+    Filter objects by lifetime?:Yes
+    Filter using a minimum lifetime?:No
+    Minimum lifetime:1
+    Filter using a maximum lifetime?:No
+    Maximum lifetime:100
+    Mitosis alternative cost:80
+    Maximum mitosis distance, in pixel units:40
+    Average cell diameter in pixels:36.0
+    Use advanced configuration parameters:Yes
+    Cost of cell to empty matching:11.0
+    Weight of area difference in function matching cost:20.0
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/track_object_lap_velocity.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,85 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+TrackObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\'Track the embryos across images using the Overlap method\x3A tracked objects are identified by the amount of frame-to-frame overlap. Save an image of embryos labeled with a unique number across time.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Choose a tracking method:LAP
+    Select the objects to track:DNA
+    Select object measurement to use for tracking:None
+    Maximum pixel distance to consider matches:50
+    Select display option:Color and Number
+    Save color-coded image?:Yes
+    Name the output image:OutputImage
+    Select the movement model:Velocity
+    Number of standard deviations for search radius:4.0
+    Search radius limit, in pixel units (Min,Max):5.0,11.0
+    Run the second phase of the LAP algorithm?:Yes
+    Gap closing cost:6
+    Split alternative cost:6
+    Merge alternative cost:6
+    Maximum gap displacement, in pixel units:6
+    Maximum split score:6
+    Maximum merge score:6
+    Maximum temporal gap, in frames:6
+    Filter objects by lifetime?:Yes
+    Filter using a minimum lifetime?:Yes
+    Minimum lifetime:1
+    Filter using a maximum lifetime?:Yes
+    Maximum lifetime:100
+    Mitosis alternative cost:6
+    Maximum mitosis distance, in pixel units:6
+    Average cell diameter in pixels:35.0
+    Use advanced configuration parameters:No
+    Cost of cell to empty matching:15.0
+    Weight of area difference in function matching cost:25.0
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/track_object_measurement_intensity.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,85 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+TrackObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\'Track the embryos across images using the Overlap method\x3A tracked objects are identified by the amount of frame-to-frame overlap. Save an image of embryos labeled with a unique number across time.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Choose a tracking method:Measurements
+    Select the objects to track:DNA
+    Select object measurement to use for tracking:Intensity_MADIntensity_Image1
+    Maximum pixel distance to consider matches:40
+    Select display option:Color only
+    Save color-coded image?:No
+    Name the output image:TrackedCells
+    Select the movement model:Both
+    Number of standard deviations for search radius:3.0
+    Search radius limit, in pixel units (Min,Max):2.0,10.0
+    Run the second phase of the LAP algorithm?:Yes
+    Gap closing cost:40
+    Split alternative cost:40
+    Merge alternative cost:40
+    Maximum gap displacement, in pixel units:5
+    Maximum split score:50
+    Maximum merge score:50
+    Maximum temporal gap, in frames:5
+    Filter objects by lifetime?:Yes
+    Filter using a minimum lifetime?:No
+    Minimum lifetime:1
+    Filter using a maximum lifetime?:Yes
+    Maximum lifetime:120
+    Mitosis alternative cost:80
+    Maximum mitosis distance, in pixel units:40
+    Average cell diameter in pixels:35.0
+    Use advanced configuration parameters:No
+    Cost of cell to empty matching:15.0
+    Weight of area difference in function matching cost:25.0
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/track_object_overlap_no_filter_max.cppipe	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,85 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+TrackObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\'Track the embryos across images using the Overlap method\x3A tracked objects are identified by the amount of frame-to-frame overlap. Save an image of embryos labeled with a unique number across time.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Choose a tracking method:Overlap
+    Select the objects to track:DNA
+    Select object measurement to use for tracking:None
+    Maximum pixel distance to consider matches:40
+    Select display option:Color only
+    Save color-coded image?:Yes
+    Name the output image:ColorCodedImage
+    Select the movement model:Both
+    Number of standard deviations for search radius:3.0
+    Search radius limit, in pixel units (Min,Max):2.0,10.0
+    Run the second phase of the LAP algorithm?:Yes
+    Gap closing cost:40
+    Split alternative cost:40
+    Merge alternative cost:40
+    Maximum gap displacement, in pixel units:5
+    Maximum split score:50
+    Maximum merge score:50
+    Maximum temporal gap, in frames:5
+    Filter objects by lifetime?:Yes
+    Filter using a minimum lifetime?:Yes
+    Minimum lifetime:2
+    Filter using a maximum lifetime?:No
+    Maximum lifetime:100
+    Mitosis alternative cost:80
+    Maximum mitosis distance, in pixel units:40
+    Average cell diameter in pixels:35.0
+    Use advanced configuration parameters:No
+    Cost of cell to empty matching:15.0
+    Weight of area difference in function matching cost:25.0
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tile.py	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,100 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+
+from cp_common_functions import get_json_value
+from cp_common_functions import get_pipeline_lines
+from cp_common_functions import get_total_number_of_modules
+from cp_common_functions import INDENTATION
+from cp_common_functions import update_module_count
+from cp_common_functions import write_pipeline
+
+
+MODULE_NAME = "Tile"
+OUTPUT_FILENAME = "output.cppipe"
+
+
+def build_header(module_name, module_number):
+    result = "|".join([f"{module_name}:[module_num:{module_number}",
+                       "svn_version:\\'Unknown\\'",
+                       "variable_revision_number:1",
+                       "show_window:True",
+                       "notes:\\x5B\\'Tile the original color image, the outlined image and the image of tracked labels together.\\'\\x5D",
+                       "batch_state:array(\\x5B\\x5D, dtype=uint8)",
+                       "enabled:True",
+                       "wants_pause:False]\n"])
+    return result
+
+
+def build_main_block(input_params):
+    result = INDENTATION.join([f"{INDENTATION}Select an input image:{get_json_value(input_params,'input_image')}\n",
+                               f"Name the output image:{get_json_value(input_params,'output_image_name')}\n",
+                               f"Tile assembly method:{get_json_value(input_params,'con_assembly_method.assembly_method')}\n"
+                               ])
+
+    calc_rows = get_json_value(input_params, 'con_assembly_method.con_calc_no_row.calc_no_row')
+    no_of_rows = 8
+
+    calc_cols = get_json_value(input_params, 'con_assembly_method.con_calc_no_cols.calc_no_cols')
+    no_of_cols = 12
+
+    if calc_rows == "No":
+        no_of_rows = get_json_value(input_params, 'con_assembly_method.con_calc_no_row.no_of_row')
+
+    if calc_cols == "No":
+        no_of_cols = get_json_value(input_params, 'con_assembly_method.con_calc_no_cols.no_of_cols')
+
+    corner_to_begin = get_json_value(input_params, 'con_assembly_method.corner_to_begin')
+    direction_tiling = get_json_value(input_params, 'con_assembly_method.direction')
+    meander = get_json_value(input_params, 'con_assembly_method.meander_mode')
+
+    assembly_method = get_json_value(input_params, 'con_assembly_method.assembly_method')
+
+    result += INDENTATION.join(
+        [f"{INDENTATION}Final number of rows:{str(no_of_rows)}\n",
+         f"Final number of columns:{str(no_of_cols)}\n",
+         f"Image corner to begin tiling:{corner_to_begin}\n",
+         f"Direction to begin tiling:{direction_tiling}\n",
+         f"Use meander mode?:{meander}\n",
+         f"Automatically calculate number of rows?:{calc_rows}\n",
+         f"Automatically calculate number of columns?:{calc_cols}\n"
+         ])
+
+    if assembly_method == "Within cycles":
+        additionals = input_params['con_assembly_method']['rpt_additional_image']
+
+        for img in additionals:
+            result += INDENTATION.join(
+                [f"{INDENTATION}Select an additional image to tile:{get_json_value(img, 'additional_img')}\n"
+                 ])
+
+    return result
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        '-p', '--pipeline',
+        help='CellProfiler pipeline'
+    )
+    parser.add_argument(
+        '-i', '--inputs',
+        help='JSON inputs from Galaxy'
+    )
+    args = parser.parse_args()
+
+    pipeline_lines = get_pipeline_lines(args.pipeline)
+    inputs_galaxy = json.load(open(args.inputs, "r"))
+
+    current_module_num = get_total_number_of_modules(pipeline_lines)
+    current_module_num += 1
+    pipeline_lines = update_module_count(pipeline_lines, current_module_num)
+
+    header_block = build_header(MODULE_NAME, current_module_num)
+    main_block = build_main_block(inputs_galaxy)
+
+    module_pipeline = f"\n{header_block}{main_block}\n"
+    pipeline_lines.append(module_pipeline)
+
+    write_pipeline(OUTPUT_FILENAME, pipeline_lines)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/track_objects.py	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,199 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+
+from cp_common_functions import get_json_value
+from cp_common_functions import get_pipeline_lines
+from cp_common_functions import get_total_number_of_modules
+from cp_common_functions import INDENTATION
+from cp_common_functions import update_module_count
+from cp_common_functions import write_pipeline
+
+MODULE_NAME = "TrackObjects"
+OUTPUT_FILENAME = "output.cppipe"
+
+
+def build_header(module_name, module_number):
+    result = "|".join([f"{module_name}:[module_num:{module_number}",
+                       "svn_version:\\'Unknown\\'",
+                       "variable_revision_number:7",
+                       "show_window:True",
+                       "notes:\\x5B\\'Track the embryos across images using the Overlap method\\x3A tracked objects are identified by the amount of frame-to-frame overlap. Save an image of embryos labeled with a unique number across time.\\'\\x5D",
+                       "batch_state:array(\\x5B\\x5D, dtype=uint8)",
+                       "enabled:True",
+                       "wants_pause:False]\n"])
+    return result
+
+
+def build_main_block(input_params):
+    result = INDENTATION.join([f"{INDENTATION}Choose a tracking method:{get_json_value(input_params,'con_tracking_method.tracking_method')}\n",
+                               f"Select the objects to track:{get_json_value(input_params,'object_to_track')}\n"
+                               ])
+
+    tracking_method = get_json_value(input_params, 'con_tracking_method.tracking_method')
+
+    obj_measurement = "None"  # default value
+    if tracking_method == "Measurements":
+        measurement_category = get_json_value(input_params, 'con_tracking_method.con_measurement_category.measurement_category')
+        measurement = get_json_value(input_params, 'con_tracking_method.con_measurement_category.measurement')
+
+        if measurement_category == "Intensity" or measurement_category == "Location":
+            img_measure = get_json_value(input_params, 'con_tracking_method.con_measurement_category.img_measure')
+            obj_measurement = f"{measurement_category}_{measurement}_{img_measure}"
+        else:
+            obj_measurement = f"{measurement_category}_{measurement}"
+
+    result += INDENTATION.join([f"{INDENTATION}Select object measurement to use for tracking:{obj_measurement}\n"])
+
+    if tracking_method == "LAP":  # no max distance required, set default for pipeline
+        max_distance = 50
+    else:
+        max_distance = get_json_value(input_params, 'con_tracking_method.max_distance')
+
+    result += INDENTATION.join([f"{INDENTATION}Maximum pixel distance to consider matches:{max_distance}\n"])
+
+    display_option = get_json_value(input_params, 'con_tracking_method.display_option')
+
+    output_img_name = "TrackedCells"  # default value, required by cppipe regardless of its presence in UI
+    save = get_json_value(input_params, 'con_tracking_method.con_save_coded_img.save_coded_img')
+    if save == "Yes":
+        output_img_name = get_json_value(input_params, 'con_tracking_method.con_save_coded_img.name_output_img')
+
+    result += INDENTATION.join(
+        [f"{INDENTATION}Select display option:{display_option}\n",
+         f"Save color-coded image?:{save}\n",
+         f"Name the output image:{output_img_name}\n"
+         ])
+
+    # LAP method default values
+    movement_model = "Both"
+    no_std = 3.0
+    radius_limit_max = 10.0
+    radius_limit_min = 2.0
+    radius = "2.0,10.0"
+    run_second = "Yes"
+    gap_closing = 40
+    split_alt = 40
+    merge_alt = 40
+    max_gap_displacement = 5
+    max_split = 50
+    max_merge = 50
+    max_temporal = 5
+    max_mitosis_dist = 40
+    mitosis_alt = 80
+
+    # LAP method
+    if tracking_method == "LAP":
+        movement_model = get_json_value(input_params, 'con_tracking_method.movement_method')
+        no_std = get_json_value(input_params, 'con_tracking_method.no_std_radius')
+        radius_limit_max = get_json_value(input_params, 'con_tracking_method.max_radius')
+        radius_limit_min = get_json_value(input_params, 'con_tracking_method.min_radius')
+        radius = f"{radius_limit_min},{radius_limit_max}"
+
+        run_second = get_json_value(input_params, 'con_tracking_method.con_second_lap.second_lap')
+        if run_second == "Yes":
+            gap_closing = get_json_value(input_params, 'con_tracking_method.con_second_lap.gap_closing')
+            split_alt = get_json_value(input_params, 'con_tracking_method.con_second_lap.split_alt')
+            merge_alt = get_json_value(input_params, 'con_tracking_method.con_second_lap.merge_alt')
+            max_gap_displacement = get_json_value(input_params, 'con_tracking_method.con_second_lap.max_gap_displacement')
+            max_split = get_json_value(input_params, 'con_tracking_method.con_second_lap.max_split')
+            max_merge = get_json_value(input_params, 'con_tracking_method.con_second_lap.max_merge')
+            max_temporal = get_json_value(input_params, 'con_tracking_method.con_second_lap.max_temporal')
+            max_mitosis_dist = get_json_value(input_params, 'con_tracking_method.con_second_lap.max_mitosis_distance')
+            mitosis_alt = get_json_value(input_params, 'con_tracking_method.con_second_lap.mitosis_alt')
+
+    result += INDENTATION.join(
+        [f"{INDENTATION}Select the movement model:{movement_model}\n",
+         f"Number of standard deviations for search radius:{no_std}\n",
+         f"Search radius limit, in pixel units (Min,Max):{radius}\n",
+         f"Run the second phase of the LAP algorithm?:{run_second}\n",
+         f"Gap closing cost:{gap_closing}\n",
+         f"Split alternative cost:{split_alt}\n",
+         f"Merge alternative cost:{merge_alt}\n",
+         f"Maximum gap displacement, in pixel units:{max_gap_displacement}\n",
+         f"Maximum split score:{max_split}\n",
+         f"Maximum merge score:{max_merge}\n",
+         f"Maximum temporal gap, in frames:{max_temporal}\n"
+         ])
+
+    # common section
+    filter_by_lifetime = get_json_value(input_params, 'con_tracking_method.con_filter_by_lifetime.filter_by_lifetime')
+    use_min = "Yes"  # default
+    min_life = 1  # default
+    use_max = "No"  # default
+    max_life = 100  # default
+
+    if filter_by_lifetime == "Yes":
+        use_min = get_json_value(input_params, 'con_tracking_method.con_filter_by_lifetime.con_use_min.use_min')
+        if use_min == "Yes":
+            min_life = get_json_value(input_params, 'con_tracking_method.con_filter_by_lifetime.con_use_min.min_lifetime')
+
+        use_max = get_json_value(input_params, 'con_tracking_method.con_filter_by_lifetime.con_use_max.use_max')
+        if use_max == "Yes":
+            max_life = get_json_value(input_params, 'con_tracking_method.con_filter_by_lifetime.con_use_max.max_lifetime')
+
+    result += INDENTATION.join(
+        [f"{INDENTATION}Filter objects by lifetime?:{filter_by_lifetime}\n",
+         f"Filter using a minimum lifetime?:{use_min}\n",
+         f"Minimum lifetime:{min_life}\n",
+         f"Filter using a maximum lifetime?:{use_max}\n",
+         f"Maximum lifetime:{max_life}\n"
+         ])
+
+    # print 2 leftover from LAP
+    result += INDENTATION.join(
+        [f"{INDENTATION}Mitosis alternative cost:{mitosis_alt}\n",
+         f"Maximum mitosis distance, in pixel units:{max_mitosis_dist}\n"
+         ])
+
+    # Follow Neighbors
+    # defaults
+    avg_cell_diameter = 35.0
+    use_adv = "No"
+    cost_of_cell = 15.0
+    weight_of_area_diff = 25.0
+
+    if tracking_method == "Follow Neighbors":
+        avg_cell_diameter = get_json_value(input_params, 'con_tracking_method.avg_diameter')
+        use_adv = get_json_value(input_params, 'con_tracking_method.con_adv_parameter.adv_parameter')
+        if use_adv == "Yes":
+            cost_of_cell = get_json_value(input_params, 'con_tracking_method.con_adv_parameter.cost')
+            weight_of_area_diff = get_json_value(input_params, 'con_tracking_method.con_adv_parameter.weight')
+
+    result += INDENTATION.join(
+        [f"{INDENTATION}Average cell diameter in pixels:{avg_cell_diameter}\n",
+         f"Use advanced configuration parameters:{use_adv}\n",
+         f"Cost of cell to empty matching:{cost_of_cell}\n",
+         f"Weight of area difference in function matching cost:{weight_of_area_diff}\n"
+         ])
+
+    return result
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        '-p', '--pipeline',
+        help='CellProfiler pipeline'
+    )
+    parser.add_argument(
+        '-i', '--inputs',
+        help='JSON inputs from Galaxy'
+    )
+    args = parser.parse_args()
+
+    pipeline_lines = get_pipeline_lines(args.pipeline)
+    inputs_galaxy = json.load(open(args.inputs, "r"))
+
+    current_module_num = get_total_number_of_modules(pipeline_lines)
+    current_module_num += 1
+    pipeline_lines = update_module_count(pipeline_lines, current_module_num)
+
+    header_block = build_header(MODULE_NAME, current_module_num)
+    main_block = build_main_block(inputs_galaxy)
+
+    module_pipeline = f"\n{header_block}{main_block}\n"
+    pipeline_lines.append(module_pipeline)
+
+    write_pipeline(OUTPUT_FILENAME, pipeline_lines)