# HG changeset patch # User bgruening # Date 1589197618 14400 # Node ID 08a2cf887a443e2dd2d415cbf996568b029a8a47 # Parent 4dcd464c22ff86c2bd8431cf7f3021e6515d3488 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb" diff -r 4dcd464c22ff -r 08a2cf887a44 macros.xml --- a/macros.xml Thu Apr 16 05:33:18 2020 -0400 +++ b/macros.xml Mon May 11 07:46:58 2020 -0400 @@ -25,12 +25,12 @@ - - + + - + @@ -81,25 +81,13 @@ - - - - - - + - - - This tool appends the inputs of the @MODULE@ module to an existing pipeline file (.cppipe) - - Input: existing pipeline file - - Output: new pipeline file - - Combine this tool with "Common" tool and "CellProfiler" tool together to run the current module alone. - + + + diff -r 4dcd464c22ff -r 08a2cf887a44 measure_image_quality.xml --- a/measure_image_quality.xml Thu Apr 16 05:33:18 2020 -0400 +++ b/measure_image_quality.xml Mon May 11 07:46:58 2020 -0400 @@ -1,24 +1,36 @@ measure features that indicate image quality - + macros.xml + + - Otsu: Thresholds for all combinations of class number, minimization parameter and middle class assignment are computed. +
- Mixture of Gaussians (MoG): Thresholds for image coverage fractions of 0.05, 0.25, 0.75 and 0.95 are computed. + See the IdentifyPrimaryObjects module for more information on thresholding methods. + ]]> + - + + + This setting allows you to apply automatic thresholding methods used in the Identify modules. + Only the global methods are applied. For more help on thresholding, see the Identify modules. + - - + + @@ -46,6 +58,13 @@ + + Select Two classes if the grayscale levels are readily distinguishable into foreground (i.e., objects) and background. + Select Three classes if there is a middle set of grayscale levels that belongs to neither the foreground nor background. + For example, three-class thresholding may be useful for images in which you have nuclear staining along with a low-intensity non-specific cell staining. + Where two-class thresholding might incorrectly assign this intermediate staining to the nuclei objects, three-class thresholding allows you to assign it to the foreground or background as desired. + However, in extreme cases where either there are almost no objects or the entire field of view is covered with objects, three-class thresholding may perform worse than two-class. + @@ -63,7 +82,7 @@ - + @@ -110,10 +129,10 @@ all_method = "No" else: all_method = params['con_calc_threshold']['con_use_all_methods']['use_all_methods'] - if all_method == "No": - threshold_count = 1 - else: - threshold_count = len(params['con_calc_threshold']['con_use_all_methods']['rpt_threshold_method']) + if all_method == "No": + threshold_count = 1 + else: + threshold_count = len(params['con_calc_threshold']['con_use_all_methods']['rpt_threshold_method']) _str += FOURSPACES + "Threshold count:%d\n" % threshold_count @@ -142,19 +161,15 @@ if all_method == "No": for method in params['con_calc_threshold']['con_use_all_methods']['rpt_threshold_method']: _str += FOURSPACES + "Select a thresholding method:%s\n" % method['con_threshold_methods']['select_threshold_method'] - - fraction_cover = method['con_threshold_methods']['mog_fraction_cover'] if 'mog_fraction_cover' in method[ - 'con_threshold_methods'] else 0.1 + + fraction_cover = method['con_threshold_methods']['mog_fraction_cover'] if 'mog_fraction_cover' in method['con_threshold_methods'] else 0.1 - tt_classes = method['con_threshold_methods']['con_threshold_classes'][ - 'threshold_classes'] if 'con_threshold_classes' in method['con_threshold_methods'] else 'Two classes' + tt_classes = method['con_threshold_methods']['con_threshold_classes']['threshold_classes'] if 'con_threshold_classes' in method['con_threshold_methods'] else 'Two classes' - minimize = method['con_threshold_methods']['otsu_weighted_entropy'] if 'otsu_weighted_entropy' in method[ - 'con_threshold_methods'] else 'Entropy' + minimize = method['con_threshold_methods']['otsu_weighted_entropy'] if 'otsu_weighted_entropy' in method['con_threshold_methods'] else 'Entropy' if tt_classes == "Three classes": - pixel_intensity = method['con_threshold_methods']['con_threshold_classes'][ - 'pixel_foreground_or_background'] + pixel_intensity = method['con_threshold_methods']['con_threshold_classes']['pixel_foreground_or_background'] else: pixel_intensity = "Foreground" @@ -177,20 +192,25 @@ new_count = module_count + 1 lines[4] = k + ":%d\n" % new_count - with open("output", "w") as f: + with open("output.cppipe", "w") as f: f.writelines(lines) f.write(writemiq()) -f.close() - + f.close() + - + - + + + Image names are separated by comma and correspond to the values in the section NameAndType of the 'Starting module' tool. + + - + + @@ -198,27 +218,42 @@ - + - - + + + + Enter an integer for the window size N, in units of pixels. The LocalFocusScore is measured within an N × N pixel window applied to the image, and the Correlation of a pixel is measured with respect to its neighbors N pixels away. + A higher number for the window size N measures larger patterns of image blur whereas smaller numbers measure more localized patterns of blur. We suggest selecting a window size that is on the order of the feature of interest (e.g., the object diameter). You can measure these metrics for multiple window sizes by selecting additional scales for each image. + + - + + + Select 'Yes' to calculate image-based intensity measures, namely the mean, maximum, minimum, standard deviation and median absolute deviation of pixel intensities. These measures are identical to those calculated by MeasureImageIntensity. + + + Select 'Yes' to calculate the saturation metrics PercentMaximal and PercentMinimal, i.e., the percentage of pixels at the upper or lower limit of each individual image. + For this calculation, the hard limits of 0 and 1 are not used because images often have undergone some kind of transformation such that no pixels ever reach the absolute maximum or minimum of the image format. Given the noise typical in images, both these measures should be a low percentage but if the images were saturated during imaging, a higher than usual PercentMaximal will be observed, and if there are no objects, the PercentMinimal value will increase. + + + Automatically calculate a suggested threshold for each image. One indicator of image quality is that these threshold values lie within a typical range. Outlier images with high or low thresholds often contain artifacts. + @@ -231,13 +266,13 @@ - + - + @@ -250,27 +285,41 @@ - - - + + + - - - - - - - - - + + + + + + + + - - - - + + + + + - - - + + + + + + diff -r 4dcd464c22ff -r 08a2cf887a44 starting_modules.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/starting_modules.py Mon May 11 07:46:58 2020 -0400 @@ -0,0 +1,227 @@ +import json +import sys +import os + +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.*)_(?P\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P\x5B0-9\x5D)_w(?P\x5B0-9\x5D)\n" + _str += FOURSPACES + "Regular expression to extract from folder name:(?P\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.*)" + elif "folder_name_regex" in methods["con_metadata_source"]: + file_regex = "(?P.*)_(?P[a-zA-Z0-9]+)" + folder_regex = methods["con_metadata_source"]["folder_name_regex"] + else: + # default regex + file_regex = "(?P.*)_(?P[a-zA-Z0-9]+)" + folder_regex = "(?P.*)" + + _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() \ No newline at end of file diff -r 4dcd464c22ff -r 08a2cf887a44 starting_modules_groups.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/starting_modules_groups.xml Mon May 11 07:46:58 2020 -0400 @@ -0,0 +1,32 @@ + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + \ No newline at end of file diff -r 4dcd464c22ff -r 08a2cf887a44 starting_modules_image.xml diff -r 4dcd464c22ff -r 08a2cf887a44 starting_modules_images.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/starting_modules_images.xml Mon May 11 07:46:58 2020 -0400 @@ -0,0 +1,10 @@ + + +
+ + + + +
+ + \ No newline at end of file diff -r 4dcd464c22ff -r 08a2cf887a44 starting_modules_metadata.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/starting_modules_metadata.xml Mon May 11 07:46:58 2020 -0400 @@ -0,0 +1,92 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + diff -r 4dcd464c22ff -r 08a2cf887a44 starting_modules_nameandtypes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/starting_modules_nameandtypes.xml Mon May 11 07:46:58 2020 -0400 @@ -0,0 +1,182 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/common-complicated.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/common-complicated.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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.*)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*)_(?P[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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/common-nogroup.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/common-nogroup.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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.*)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*)_(?P[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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/common.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/common.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/common.txt --- a/test-data/common.txt Thu Apr 16 05:33:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) - Regular expression to extract from folder name:(?P.*) - 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/convert_objects_to_image.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/convert_objects_to_image.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/convert_objects_to_image.txt --- a/test-data/convert_objects_to_image.txt Thu Apr 16 05:33:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,59 +0,0 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) - Regular expression to extract from folder name:(?P.*) - 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 - -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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/display_data_on_image.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/display_data_on_image.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/display_data_on_image.txt --- a/test-data/display_data_on_image.txt Thu Apr 16 05:33:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,70 +0,0 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) - Regular expression to extract from folder name:(?P.*) - 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 - -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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/enhance_or_suppress_features.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/enhance_or_suppress_features.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/enhance_or_suppress_features.txt --- a/test-data/enhance_or_suppress_features.txt Thu Apr 16 05:33:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,66 +0,0 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) - Regular expression to extract from folder name:(?P.*) - 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 - -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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/export_to_spreadsheet.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/export_to_spreadsheet.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/export_to_spreadsheet.txt --- a/test-data/export_to_spreadsheet.txt Thu Apr 16 05:33:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) - Regular expression to extract from folder name:(?P.*) - 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 - -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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/export_to_spreadsheet_create_gene.cppipe diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/export_to_spreadsheet_create_gene_image_filename.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/export_to_spreadsheet_create_gene_image_filename.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/export_to_spreadsheet_create_gene_metadata.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/export_to_spreadsheet_create_gene_metadata.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/export_to_spreadsheet_multi.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/export_to_spreadsheet_multi.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/gray_to_color.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gray_to_color.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/gray_to_color.txt --- a/test-data/gray_to_color.txt Thu Apr 16 05:33:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,75 +0,0 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) - Regular expression to extract from folder name:(?P.*) - 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 - -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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/identify_primary_objects.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/identify_primary_objects.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/identify_primary_objects.txt --- a/test-data/identify_primary_objects.txt Thu Apr 16 05:33:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,88 +0,0 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) - Regular expression to extract from folder name:(?P.*) - 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\'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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/identify_primary_objects_adv_adaptive_otsu.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/identify_primary_objects_adv_adaptive_otsu.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/identify_primary_objects_adv_global_manual.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/identify_primary_objects_adv_global_manual.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/identify_primary_objects_adv_global_mce.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/identify_primary_objects_adv_global_mce.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/identify_primary_objects_adv_global_measurement.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/identify_primary_objects_adv_global_measurement.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/identify_primary_objects_adv_global_rb.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/identify_primary_objects_adv_global_rb.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/identify_primary_objects_noadv.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/identify_primary_objects_noadv.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/image_math.xml diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/images.tar Binary file test-data/images.tar has changed diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/mask_image.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mask_image.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/mask_image.txt --- a/test-data/mask_image.txt Thu Apr 16 05:33:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) - Regular expression to extract from folder name:(?P.*) - 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 - -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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/measure_granularity.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/measure_granularity.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/measure_granularity.txt --- a/test-data/measure_granularity.txt Thu Apr 16 05:33:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,62 +0,0 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) - Regular expression to extract from folder name:(?P.*) - 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 - -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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/measure_image_area_occupied.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/measure_image_area_occupied.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/measure_image_area_occupied.txt --- a/test-data/measure_image_area_occupied.txt Thu Apr 16 05:33:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,62 +0,0 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) - Regular expression to extract from folder name:(?P.*) - 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 - -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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/measure_image_intensity.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/measure_image_intensity.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/measure_image_intensity.txt --- a/test-data/measure_image_intensity.txt Thu Apr 16 05:33:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) - Regular expression to extract from folder name:(?P.*) - 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 - -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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/measure_image_quality.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/measure_image_quality.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/measure_image_quality.txt --- a/test-data/measure_image_quality.txt Thu Apr 16 05:33:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,72 +0,0 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) - Regular expression to extract from folder name:(?P.*) - 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 - -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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/measure_object_intensity.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/measure_object_intensity.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/measure_object_intensity.txt --- a/test-data/measure_object_intensity.txt Thu Apr 16 05:33:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,58 +0,0 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) - Regular expression to extract from folder name:(?P.*) - 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 - -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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/measure_object_size.txt diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/measure_object_size_shape.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/measure_object_size_shape.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/measure_object_size_shape.txt --- a/test-data/measure_object_size_shape.txt Thu Apr 16 05:33:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,58 +0,0 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) - Regular expression to extract from folder name:(?P.*) - 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 - -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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/measure_texture.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/measure_texture.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/measure_texture.txt --- a/test-data/measure_texture.txt Thu Apr 16 05:33:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,62 +0,0 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) - Regular expression to extract from folder name:(?P.*) - 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 - -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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/relate_objects.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relate_objects.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/relate_objects.txt --- a/test-data/relate_objects.txt Thu Apr 16 05:33:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,62 +0,0 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) - Regular expression to extract from folder name:(?P.*) - 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 - -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 diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/save_images.cppipe --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/save_images.cppipe Mon May 11 07:46:58 2020 -0400 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) + Regular expression to extract from folder name:(?P.*) + 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... diff -r 4dcd464c22ff -r 08a2cf887a44 test-data/save_images.txt --- a/test-data/save_images.txt Thu Apr 16 05:33:18 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,71 +0,0 @@ -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.*)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+)_(?P[a-zA-Z0-9]+) - Regular expression to extract from folder name:(?P.*) - 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 - -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...