Mercurial > repos > bgruening > cp_overlay_outlines

annotate test-data/image_math_3.cppipe @ 2:b44b081bcf37 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sun, 05 Nov 2023 09:39:27 +0000
parents 91560258e972
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
1 CellProfiler Pipeline: http://www.cellprofiler.org
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
2 Version:3
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
3 DateRevision:319
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
4 GitHash:
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
5 ModuleCount:7
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
6 HasImagePlaneDetails:False
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
7
1
91560258e972 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
bgruening
parents: 0
diff changeset
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]
0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
9 :
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
10 Filter images?:Images only
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
11 Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
12
1
91560258e972 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
bgruening
parents: 0
diff changeset
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]
0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
14 Extract metadata?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
15 Metadata data type:Text
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
16 Metadata types:{}
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
17 Extraction method count:1
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
18 Metadata extraction method:Extract from file/folder names
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
19 Metadata source:File name
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
20 Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
21 Regular expression to extract from folder name:(?P<field1>.*)
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
22 Extract metadata from:All images
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
23 Select the filtering criteria:and (file does contain "")
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
24 Metadata file location:
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
25 Match file and image metadata:[]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
26 Use case insensitive matching?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
27
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
28 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]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
29 Assign a name to:Images matching rules
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
30 Select the image type:Grayscale image
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
31 Name to assign these images:DNA
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
32 Match metadata:[]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
33 Image set matching method:Order
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
34 Set intensity range from:Image metadata
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
35 Assignments count:1
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
36 Single images count:0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
37 Maximum intensity:255.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
38 Process as 3D?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
39 Relative pixel spacing in X:1.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
40 Relative pixel spacing in Y:1.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
41 Relative pixel spacing in Z:1.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
42 Select the rule criteria:and (file does startwith "im")
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
43 Name to assign these images:DNA
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
44 Name to assign these objects:Cell
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
45 Select the image type:Grayscale image
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
46 Set intensity range from:Image metadata
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
47 Select the image type:Grayscale image
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
48 Maximum intensity:255.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
49
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
50 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]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
51 Do you want to group your images?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
52 grouping metadata count:1
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
53 Metadata category:Screen
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
54
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
55 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]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
56 Select the input image:DNA
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
57 Name the primary objects to be identified:Nucleus
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
58 Typical diameter of objects, in pixel units (Min,Max):15,200
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
59 Discard objects outside the diameter range?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
60 Discard objects touching the border of the image?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
61 Method to distinguish clumped objects:Intensity
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
62 Method to draw dividing lines between clumped objects:Intensity
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
63 Size of smoothing filter:10
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
64 Suppress local maxima that are closer than this minimum allowed distance:7.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
65 Speed up by using lower-resolution image to find local maxima?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
66 Fill holes in identified objects?:After both thresholding and declumping
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
67 Automatically calculate size of smoothing filter for declumping?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
68 Automatically calculate minimum allowed distance between local maxima?:Yes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
69 Handling of objects if excessive number of objects identified:Continue
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
70 Maximum number of objects:500
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
71 Use advanced settings?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
72 Threshold setting version:10
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
73 Threshold strategy:Global
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
74 Thresholding method:Minimum cross entropy
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
75 Threshold smoothing scale:1.3488
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
76 Threshold correction factor:1.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
77 Lower and upper bounds on threshold:0.0,1.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
78 Manual threshold:0.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
79 Select the measurement to threshold with:None
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
80 Two-class or three-class thresholding?:Two classes
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
81 Assign pixels in the middle intensity class to the foreground or the background?:Foreground
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
82 Size of adaptive window:50
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
83 Lower outlier fraction:0.05
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
84 Upper outlier fraction:0.05
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
85 Averaging method:Mean
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
86 Variance method:Standard deviation
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
87 # of deviations:2.0
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
88 Thresholding method:Otsu
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
89
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
90 ConvertObjectsToImage:[module_num:6|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
91 Select the input objects:Nucleus
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
92 Name the output image:CellImage
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
93 Select the color format:Binary (black & white)
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
94 Select the colormap:Default
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
95
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
96 ImageMath:[module_num:7|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
97 Operation:Not
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
98 Raise the power of the result by:
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
99 Multiply the result by:
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
100 Add to result:
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
101 Set values less than 0 equal to 0?:
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
102 Set values greater than 1 equal to 1?:
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
103 Ignore the image masks?:No
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
104 Name the output image:ImageAfterMath
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
105 Image or measurement?:Image
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
106 Select the first image:DNA
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
107 Multiply the first image by:
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
108 Measurement:
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
109 Image or measurement?:
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
110 Select the second image:
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
111 Multiply the second image by:
39006f6fd6bf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
112 Measurement: