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comparison test-data/track_object.cppipe @ 4:e7273daa5ae2 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 10:01:41 +0000
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children 670975e92458
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3:27396311a314 4:e7273daa5ae2
1 CellProfiler Pipeline: http://www.cellprofiler.org
2 Version:3
3 DateRevision:319
4 GitHash:
5 ModuleCount:5
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.\']|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 startwith ".")
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.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
14 Extract metadata?:Yes
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<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
21 Regular expression to extract from folder name:(?P<folderField1>.*)
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:[]
26 Use case insensitive matching?:No
27
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]
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:[]
33 Image set matching method:Order
34 Set intensity range from:Image metadata
35 Assignments count:1
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 startwith "im")
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 Select the image type:Grayscale image
48 Maximum intensity:255.0
49
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]
51 Do you want to group your images?:Yes
52 grouping metadata count:1
53 Metadata category:field1
54
55 TrackObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:7|show_window:True|notes:\x5B\'Track the embryos across images using the Overlap method\x3A tracked objects are identified by the amount of frame-to-frame overlap. Save an image of embryos labeled with a unique number across time.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
56 Choose a tracking method:Overlap
57 Select the objects to track:Embryos
58 Select object measurement to use for tracking:None
59 Maximum pixel distance to consider matches:50
60 Select display option:Color and Number
61 Save color-coded image?:Yes
62 Name the output image:TrackedCells
63 Select the movement model:Both
64 Number of standard deviations for search radius:3.0
65 Search radius limit, in pixel units (Min,Max):2.0,10.0
66 Run the second phase of the LAP algorithm?:Yes
67 Gap closing cost:40
68 Split alternative cost:40
69 Merge alternative cost:40
70 Maximum gap displacement, in pixel units:5
71 Maximum split score:50
72 Maximum merge score:50
73 Maximum temporal gap, in frames:5
74 Filter objects by lifetime?:No
75 Filter using a minimum lifetime?:Yes
76 Minimum lifetime:1
77 Filter using a maximum lifetime?:No
78 Maximum lifetime:100
79 Mitosis alternative cost:80
80 Maximum mitosis distance, in pixel units:40
81 Average cell diameter in pixels:35.0
82 Use advanced configuration parameters:No
83 Cost of cell to empty matching:15.0
84 Weight of area difference in function matching cost:25.0
85