Mercurial > repos > bgruening > cp_cellprofiler4

comparison test-data/ExampleHuman.cppipe @ 0:b333df978624 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
author bgruening
date Mon, 25 Apr 2022 18:30:59 +0000
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1 CellProfiler Pipeline: http://www.cellprofiler.org
2 Version:5
3 DateRevision:400
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:['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]
9 :
10 Filter images?:Images only
11 Select the rule criteria:and (extension does isimage) (directory doesnot containregexp "[\\\\\\\\/]\\\\.")
12
13 Metadata:[module_num:2|svn_version:'Unknown'|variable_revision_number:6|show_window:False|notes:['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]
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>[A-P][0-9]{2})_s(?P<Site>[0-9])_w(?P<ChannelNumber>[0-9])
21 Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
22 Extract metadata from:All images
23 Select the filtering criteria:and (file does contain "")
24 Metadata file location:Elsewhere...|
25 Match file and image metadata:[]
26 Use case insensitive matching?:No
27 Metadata file name:
28 Does cached metadata exist?:No
29
30 NamesAndTypes:[module_num:3|svn_version:'Unknown'|variable_revision_number:8|show_window:False|notes:['DNA: DNA stained with DAPI', 'PH3: An antibody for phosphorylated histone H3 correlated with mitosis', 'cellbody: ']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
31 Assign a name to:Images matching rules
32 Select the image type:Grayscale image
33 Name to assign these images:DNA
34 Match metadata:[]
35 Image set matching method:Order
36 Set intensity range from:Image metadata
37 Assignments count:3
38 Single images count:0
39 Maximum intensity:255.0
40 Process as 3D?:No
41 Relative pixel spacing in X:1.0
42 Relative pixel spacing in Y:1.0
43 Relative pixel spacing in Z:1.0
44 Select the rule criteria:and (file does contain "d0.tif")
45 Name to assign these images:DNA
46 Name to assign these objects:Cell
47 Select the image type:Grayscale image
48 Set intensity range from:Image metadata
49 Maximum intensity:255.0
50 Select the rule criteria:and (file does contain "d1.tif")
51 Name to assign these images:PH3
52 Name to assign these objects:Cell
53 Select the image type:Grayscale image
54 Set intensity range from:Image metadata
55 Maximum intensity:255.0
56 Select the rule criteria:and (file does contain "d2.tif")
57 Name to assign these images:cellbody
58 Name to assign these objects:Cell
59 Select the image type:Grayscale image
60 Set intensity range from:Image metadata
61 Maximum intensity:255.0
62
63 Groups:[module_num:4|svn_version:'Unknown'|variable_revision_number:2|show_window:False|notes:['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.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
64 Do you want to group your images?:No
65 grouping metadata count:1
66 Metadata category:None
67
68 IdentifyPrimaryObjects:[module_num:5|svn_version:'Unknown'|variable_revision_number:14|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
69 Select the input image:DNA
70 Name the primary objects to be identified:Nuclei
71 Typical diameter of objects, in pixel units (Min,Max):8,80
72 Discard objects outside the diameter range?:Yes
73 Discard objects touching the border of the image?:Yes
74 Method to distinguish clumped objects:Intensity
75 Method to draw dividing lines between clumped objects:Intensity
76 Size of smoothing filter:10
77 Suppress local maxima that are closer than this minimum allowed distance:7.0
78 Speed up by using lower-resolution image to find local maxima?:Yes
79 Fill holes in identified objects?:After declumping only
80 Automatically calculate size of smoothing filter for declumping?:Yes
81 Automatically calculate minimum allowed distance between local maxima?:Yes
82 Handling of objects if excessive number of objects identified:Continue
83 Maximum number of objects:500
84 Display accepted local maxima?:No
85 Select maxima color:Blue
86 Use advanced settings?:No
87 Threshold setting version:11
88 Threshold strategy:Global
89 Thresholding method:Minimum Cross-Entropy
90 Threshold smoothing scale:1.3488
91 Threshold correction factor:1.0
92 Lower and upper bounds on threshold:0.0,1.0
93 Manual threshold:0.0
94 Select the measurement to threshold with:None
95 Two-class or three-class thresholding?:Two classes
96 Assign pixels in the middle intensity class to the foreground or the background?:Foreground
97 Size of adaptive window:50
98 Lower outlier fraction:0.05
99 Upper outlier fraction:0.05
100 Averaging method:Mean
101 Variance method:Standard deviation
102 # of deviations:2.0
103 Thresholding method:Otsu
104
105 IdentifyPrimaryObjects:[module_num:6|svn_version:'Unknown'|variable_revision_number:14|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
106 Select the input image:PH3
107 Name the primary objects to be identified:PH3
108 Typical diameter of objects, in pixel units (Min,Max):7,80
109 Discard objects outside the diameter range?:Yes
110 Discard objects touching the border of the image?:Yes
111 Method to distinguish clumped objects:Intensity
112 Method to draw dividing lines between clumped objects:Intensity
113 Size of smoothing filter:10
114 Suppress local maxima that are closer than this minimum allowed distance:7.0
115 Speed up by using lower-resolution image to find local maxima?:Yes
116 Fill holes in identified objects?:After declumping only
117 Automatically calculate size of smoothing filter for declumping?:Yes
118 Automatically calculate minimum allowed distance between local maxima?:Yes
119 Handling of objects if excessive number of objects identified:Continue
120 Maximum number of objects:500
121 Display accepted local maxima?:No
122 Select maxima color:Blue
123 Use advanced settings?:Yes
124 Threshold setting version:11
125 Threshold strategy:Global
126 Thresholding method:Otsu
127 Threshold smoothing scale:1.3488
128 Threshold correction factor:1.0
129 Lower and upper bounds on threshold:0.0,1.0
130 Manual threshold:0.0
131 Select the measurement to threshold with:None
132 Two-class or three-class thresholding?:Three classes
133 Assign pixels in the middle intensity class to the foreground or the background?:Foreground
134 Size of adaptive window:50
135 Lower outlier fraction:0.05
136 Upper outlier fraction:0.05
137 Averaging method:Mean
138 Variance method:Standard deviation
139 # of deviations:2.0
140 Thresholding method:Otsu
141
142 RelateObjects:[module_num:7|svn_version:'Unknown'|variable_revision_number:5|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
143 Parent objects:Nuclei
144 Child objects:PH3
145 Calculate child-parent distances?:None
146 Calculate per-parent means for all child measurements?:No
147 Calculate distances to other parents?:No
148 Do you want to save the children with parents as a new object set?:No
149 Name the output object:None
150 Parent name:None
151 Parent name:None
152
153 IdentifySecondaryObjects:[module_num:8|svn_version:'Unknown'|variable_revision_number:10|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
154 Select the input objects:Nuclei
155 Name the objects to be identified:Cells
156 Select the method to identify the secondary objects:Propagation
157 Select the input image:cellbody
158 Number of pixels by which to expand the primary objects:10
159 Regularization factor:0.05
160 Discard secondary objects touching the border of the image?:No
161 Discard the associated primary objects?:No
162 Name the new primary objects:FilteredNuclei
163 Fill holes in identified objects?:Yes
164 Threshold setting version:11
165 Threshold strategy:Global
166 Thresholding method:Minimum Cross-Entropy
167 Threshold smoothing scale:0.0
168 Threshold correction factor:0.8
169 Lower and upper bounds on threshold:0.0,1.0
170 Manual threshold:0.0
171 Select the measurement to threshold with:None
172 Two-class or three-class thresholding?:Three classes
173 Assign pixels in the middle intensity class to the foreground or the background?:Foreground
174 Size of adaptive window:50
175 Lower outlier fraction:0.05
176 Upper outlier fraction:0.05
177 Averaging method:Mean
178 Variance method:Standard deviation
179 # of deviations:2.0
180 Thresholding method:Otsu
181
182 IdentifyTertiaryObjects:[module_num:9|svn_version:'Unknown'|variable_revision_number:3|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
183 Select the larger identified objects:Cells
184 Select the smaller identified objects:Nuclei
185 Name the tertiary objects to be identified:Cytoplasm
186 Shrink smaller object prior to subtraction?:Yes
187
188 MeasureObjectIntensity:[module_num:10|svn_version:'Unknown'|variable_revision_number:4|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
189 Select images to measure:DNA, PH3
190 Select objects to measure:Nuclei, Cells, Cytoplasm
191
192 MeasureObjectSizeShape:[module_num:11|svn_version:'Unknown'|variable_revision_number:3|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
193 Select object sets to measure:Nuclei, Cells, Cytoplasm
194 Calculate the Zernike features?:Yes
195 Calculate the advanced features?:No
196
197 OverlayOutlines:[module_num:12|svn_version:'Unknown'|variable_revision_number:4|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
198 Display outlines on a blank image?:No
199 Select image on which to display outlines:DNA
200 Name the output image:OrigOverlay
201 Outline display mode:Color
202 Select method to determine brightness of outlines:Max of image
203 How to outline:Thick
204 Select outline color:#0080FF
205 Select objects to display:Cells
206 Select outline color:blue
207 Select objects to display:Nuclei
208 Select outline color:yellow
209 Select objects to display:PH3
210
211 SaveImages:[module_num:13|svn_version:'Unknown'|variable_revision_number:15|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
212 Select the type of image to save:Image
213 Select the image to save:OrigOverlay
214 Select method for constructing file names:From image filename
215 Select image name for file prefix:DNA
216 Enter single file name:OrigBlue
217 Number of digits:4
218 Append a suffix to the image file name?:Yes
219 Text to append to the image name:_Overlay
220 Saved file format:png
221 Output file location:Default Output Folder|
222 Image bit depth:8-bit integer
223 Overwrite existing files without warning?:Yes
224 When to save:Every cycle
225 Record the file and path information to the saved image?:Yes
226 Create subfolders in the output folder?:No
227 Base image folder:Elsewhere...|
228 How to save the series:T (Time)
229
230 ExportToSpreadsheet:[module_num:14|svn_version:'Unknown'|variable_revision_number:13|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
231 Select the column delimiter:Comma (",")
232 Add image metadata columns to your object data file?:No
233 Add image file and folder names to your object data file?:No
234 Select the measurements to export:No
235 Calculate the per-image mean values for object measurements?:No
236 Calculate the per-image median values for object measurements?:No
237 Calculate the per-image standard deviation values for object measurements?:No
238 Output file location:Default Output Folder|
239 Create a GenePattern GCT file?:No
240 Select source of sample row name:Metadata
241 Select the image to use as the identifier:None
242 Select the metadata to use as the identifier:None
243 Export all measurement types?:Yes
244 Press button to select measurements:
245 Representation of Nan/Inf:NaN
246 Add a prefix to file names?:No
247 Filename prefix:MyExpt_
248 Overwrite existing files without warning?:Yes
249 Data to export:Do not use
250 Combine these object measurements with those of the previous object?:No
251 File name:DATA.csv
252 Use the object name for the file name?:Yes