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comparison test-data/ExampleHuman.cppipe @ 0:33bf7aa4e684 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
author bgruening
date Sat, 06 Feb 2021 10:00:59 +0000
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1 CellProfiler Pipeline: http://www.cellprofiler.org
2 Version:3
3 DateRevision:300
4 GitHash:
5 ModuleCount:14
6 HasImagePlaneDetails:False
7
8 Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
9 :
10 Filter images?:Images only
11 Select the rule criteria:and (extension does isimage) (directory doesnot containregexp "\x5B\\\\\\\\\\\\\\\\/\x5D\\\\\\\\.")
12
13 Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
14 Extract metadata?:No
15 Metadata data type:Text
16 Metadata types:{}
17 Extraction method count:1
18 Metadata extraction method:Extract from file/folder names
19 Metadata source:File name
20 Regular expression to extract from file name:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)_w(?P<ChannelNumber>\x5B0-9\x5D)
21 Regular expression to extract from folder name:(?P<Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$
22 Extract metadata from:All images
23 Select the filtering criteria:and (file does contain "")
24 Metadata file location:
25 Match file and image metadata:\x5B\x5D
26 Use case insensitive matching?:No
27
28 NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'DNA\x3A DNA stained with DAPI\', \'PH3\x3A An antibody for phosphorylated histone H3 correlated with mitosis\', \'cellbody\x3A \'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
29 Assign a name to:Images matching rules
30 Select the image type:Grayscale image
31 Name to assign these images:DNA
32 Match metadata:\x5B\x5D
33 Image set matching method:Order
34 Set intensity range from:Image metadata
35 Assignments count:3
36 Single images count:0
37 Maximum intensity:255.0
38 Process as 3D?:No
39 Relative pixel spacing in X:1.0
40 Relative pixel spacing in Y:1.0
41 Relative pixel spacing in Z:1.0
42 Select the rule criteria:and (file does contain "d0.tif")
43 Name to assign these images:DNA
44 Name to assign these objects:Cell
45 Select the image type:Grayscale image
46 Set intensity range from:Image metadata
47 Maximum intensity:255.0
48 Select the rule criteria:and (file does contain "d1.tif")
49 Name to assign these images:PH3
50 Name to assign these objects:Cell
51 Select the image type:Grayscale image
52 Set intensity range from:Image metadata
53 Maximum intensity:255.0
54 Select the rule criteria:and (file does contain "d2.tif")
55 Name to assign these images:cellbody
56 Name to assign these objects:Cell
57 Select the image type:Grayscale image
58 Set intensity range from:Image metadata
59 Maximum intensity:255.0
60
61 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]
62 Do you want to group your images?:No
63 grouping metadata count:1
64 Metadata category:None
65
66 IdentifyPrimaryObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
67 Select the input image:DNA
68 Name the primary objects to be identified:Nuclei
69 Typical diameter of objects, in pixel units (Min,Max):8,80
70 Discard objects outside the diameter range?:Yes
71 Discard objects touching the border of the image?:Yes
72 Method to distinguish clumped objects:Intensity
73 Method to draw dividing lines between clumped objects:Intensity
74 Size of smoothing filter:10
75 Suppress local maxima that are closer than this minimum allowed distance:7.0
76 Speed up by using lower-resolution image to find local maxima?:Yes
77 Fill holes in identified objects?:After declumping only
78 Automatically calculate size of smoothing filter for declumping?:Yes
79 Automatically calculate minimum allowed distance between local maxima?:Yes
80 Handling of objects if excessive number of objects identified:Continue
81 Maximum number of objects:500
82 Use advanced settings?:No
83 Threshold setting version:10
84 Threshold strategy:Global
85 Thresholding method:Minimum cross entropy
86 Threshold smoothing scale:1.3488
87 Threshold correction factor:1.0
88 Lower and upper bounds on threshold:0.0,1.0
89 Manual threshold:0.0
90 Select the measurement to threshold with:None
91 Two-class or three-class thresholding?:Two classes
92 Assign pixels in the middle intensity class to the foreground or the background?:Foreground
93 Size of adaptive window:50
94 Lower outlier fraction:0.05
95 Upper outlier fraction:0.05
96 Averaging method:Mean
97 Variance method:Standard deviation
98 # of deviations:2.0
99 Thresholding method:Otsu
100
101 IdentifyPrimaryObjects:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
102 Select the input image:PH3
103 Name the primary objects to be identified:PH3
104 Typical diameter of objects, in pixel units (Min,Max):8,80
105 Discard objects outside the diameter range?:Yes
106 Discard objects touching the border of the image?:Yes
107 Method to distinguish clumped objects:Intensity
108 Method to draw dividing lines between clumped objects:Intensity
109 Size of smoothing filter:10
110 Suppress local maxima that are closer than this minimum allowed distance:7.0
111 Speed up by using lower-resolution image to find local maxima?:Yes
112 Fill holes in identified objects?:After declumping only
113 Automatically calculate size of smoothing filter for declumping?:Yes
114 Automatically calculate minimum allowed distance between local maxima?:Yes
115 Handling of objects if excessive number of objects identified:Continue
116 Maximum number of objects:500
117 Use advanced settings?:No
118 Threshold setting version:10
119 Threshold strategy:Global
120 Thresholding method:Minimum cross entropy
121 Threshold smoothing scale:1.3488
122 Threshold correction factor:1.0
123 Lower and upper bounds on threshold:0.0,1.0
124 Manual threshold:0.0
125 Select the measurement to threshold with:None
126 Two-class or three-class thresholding?:Two classes
127 Assign pixels in the middle intensity class to the foreground or the background?:Foreground
128 Size of adaptive window:50
129 Lower outlier fraction:0.05
130 Upper outlier fraction:0.05
131 Averaging method:Mean
132 Variance method:Standard deviation
133 # of deviations:2.0
134 Thresholding method:Otsu
135
136 RelateObjects:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
137 Parent objects:Nuclei
138 Child objects:PH3
139 Calculate child-parent distances?:None
140 Calculate per-parent means for all child measurements?:No
141 Calculate distances to other parents?:No
142 Parent name:None
143
144 IdentifySecondaryObjects:[module_num:8|svn_version:\'Unknown\'|variable_revision_number:10|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
145 Select the input objects:Nuclei
146 Name the objects to be identified:Cells
147 Select the method to identify the secondary objects:Propagation
148 Select the input image:cellbody
149 Number of pixels by which to expand the primary objects:10
150 Regularization factor:0.05
151 Discard secondary objects touching the border of the image?:No
152 Discard the associated primary objects?:No
153 Name the new primary objects:FilteredNuclei
154 Fill holes in identified objects?:Yes
155 Threshold setting version:10
156 Threshold strategy:Global
157 Thresholding method:Otsu
158 Threshold smoothing scale:0.0
159 Threshold correction factor:1.0
160 Lower and upper bounds on threshold:0.0,1.0
161 Manual threshold:0.0
162 Select the measurement to threshold with:None
163 Two-class or three-class thresholding?:Three classes
164 Assign pixels in the middle intensity class to the foreground or the background?:Foreground
165 Size of adaptive window:50
166 Lower outlier fraction:0.05
167 Upper outlier fraction:0.05
168 Averaging method:Mean
169 Variance method:Standard deviation
170 # of deviations:2.0
171 Thresholding method:Otsu
172
173 IdentifyTertiaryObjects:[module_num:9|svn_version:\'Unknown\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
174 Select the larger identified objects:Cells
175 Select the smaller identified objects:Nuclei
176 Name the tertiary objects to be identified:Cytoplasm
177 Shrink smaller object prior to subtraction?:Yes
178
179 MeasureObjectIntensity:[module_num:10|svn_version:\'Unknown\'|variable_revision_number:3|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
180 Hidden:2
181 Select an image to measure:DNA
182 Select an image to measure:PH3
183 Select objects to measure:Nuclei
184 Select objects to measure:Cells
185 Select objects to measure:Cytoplasm
186
187 MeasureObjectSizeShape:[module_num:11|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
188 Select objects to measure:Nuclei
189 Select objects to measure:Cells
190 Select objects to measure:Cytoplasm
191 Calculate the Zernike features?:Yes
192
193 OverlayOutlines:[module_num:12|svn_version:\'Unknown\'|variable_revision_number:4|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
194 Display outlines on a blank image?:No
195 Select image on which to display outlines:DNA
196 Name the output image:OrigOverlay
197 Outline display mode:Color
198 Select method to determine brightness of outlines:Max of image
199 How to outline:Thick
200 Select outline color:#0080FF
201 Select objects to display:Cells
202 Select outline color:blue
203 Select objects to display:Nuclei
204 Select outline color:yellow
205 Select objects to display:PH3
206
207 SaveImages:[module_num:13|svn_version:\'Unknown\'|variable_revision_number:13|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
208 Select the type of image to save:Image
209 Select the image to save:OrigOverlay
210 Select method for constructing file names:From image filename
211 Select image name for file prefix:DNA
212 Enter single file name:OrigBlue
213 Number of digits:4
214 Append a suffix to the image file name?:Yes
215 Text to append to the image name:_Overlay
216 Saved file format:png
217 Output file location:Default Output Folder\x7C
218 Image bit depth:8-bit integer
219 Overwrite existing files without warning?:Yes
220 When to save:Every cycle
221 Record the file and path information to the saved image?:Yes
222 Create subfolders in the output folder?:No
223 Base image folder:Elsewhere...\x7C
224
225 ExportToSpreadsheet:[module_num:14|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
226 Select the column delimiter:Comma (",")
227 Add image metadata columns to your object data file?:No
228 Select the measurements to export:No
229 Calculate the per-image mean values for object measurements?:No
230 Calculate the per-image median values for object measurements?:No
231 Calculate the per-image standard deviation values for object measurements?:No
232 Output file location:Default Output Folder\x7C
233 Create a GenePattern GCT file?:No
234 Select source of sample row name:Metadata
235 Select the image to use as the identifier:None
236 Select the metadata to use as the identifier:None
237 Export all measurement types?:Yes
238 Press button to select measurements:
239 Representation of Nan/Inf:NaN
240 Add a prefix to file names?:No
241 Filename prefix:MyExpt_
242 Overwrite existing files without warning?:Yes
243 Data to export:Do not use
244 Combine these object measurements with those of the previous object?:No
245 File name:DATA.csv
246 Use the object name for the file name?:Yes