Mercurial > repos > bgruening > cp_cellprofiler4

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit d18fae96f65d1b748fbd21b92b75ca3181fdd8bc
author bgruening
date Mon, 05 Aug 2024 15:30:07 +0000
parents b333df978624
children
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b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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1 CellProfiler Pipeline: http://www.cellprofiler.org
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2 Version:5
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3 DateRevision:400
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4 GitHash:
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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5 ModuleCount:14
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6 HasImagePlaneDetails:False
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7
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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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]
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9 :
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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10 Filter images?:Images only
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11 Select the rule criteria:and (extension does isimage) (directory doesnot containregexp "[\\\\\\\\/]\\\\.")
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12
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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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]
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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14 Extract metadata?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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15 Metadata data type:Text
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16 Metadata types:{}
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17 Extraction method count:1
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18 Metadata extraction method:Extract from file/folder names
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19 Metadata source:File name
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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])
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21 Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
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22 Extract metadata from:All images
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23 Select the filtering criteria:and (file does contain "")
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24 Metadata file location:Elsewhere...|
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25 Match file and image metadata:[]
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26 Use case insensitive matching?:No
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27 Metadata file name:
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28 Does cached metadata exist?:No
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29
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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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]
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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31 Assign a name to:Images matching rules
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32 Select the image type:Grayscale image
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33 Name to assign these images:DNA
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34 Match metadata:[]
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35 Image set matching method:Order
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36 Set intensity range from:Image metadata
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37 Assignments count:3
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38 Single images count:0
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39 Maximum intensity:255.0
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40 Process as 3D?:No
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41 Relative pixel spacing in X:1.0
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42 Relative pixel spacing in Y:1.0
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43 Relative pixel spacing in Z:1.0
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44 Select the rule criteria:and (file does contain "d0.tif")
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45 Name to assign these images:DNA
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46 Name to assign these objects:Cell
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47 Select the image type:Grayscale image
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48 Set intensity range from:Image metadata
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49 Maximum intensity:255.0
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50 Select the rule criteria:and (file does contain "d1.tif")
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51 Name to assign these images:PH3
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52 Name to assign these objects:Cell
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53 Select the image type:Grayscale image
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54 Set intensity range from:Image metadata
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55 Maximum intensity:255.0
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56 Select the rule criteria:and (file does contain "d2.tif")
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57 Name to assign these images:cellbody
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58 Name to assign these objects:Cell
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59 Select the image type:Grayscale image
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60 Set intensity range from:Image metadata
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61 Maximum intensity:255.0
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62
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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]
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64 Do you want to group your images?:No
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65 grouping metadata count:1
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66 Metadata category:None
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67
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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]
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69 Select the input image:DNA
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70 Name the primary objects to be identified:Nuclei
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71 Typical diameter of objects, in pixel units (Min,Max):8,80
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72 Discard objects outside the diameter range?:Yes
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73 Discard objects touching the border of the image?:Yes
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74 Method to distinguish clumped objects:Intensity
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75 Method to draw dividing lines between clumped objects:Intensity
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76 Size of smoothing filter:10
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77 Suppress local maxima that are closer than this minimum allowed distance:7.0
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78 Speed up by using lower-resolution image to find local maxima?:Yes
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79 Fill holes in identified objects?:After declumping only
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80 Automatically calculate size of smoothing filter for declumping?:Yes
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81 Automatically calculate minimum allowed distance between local maxima?:Yes
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82 Handling of objects if excessive number of objects identified:Continue
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83 Maximum number of objects:500
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84 Display accepted local maxima?:No
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85 Select maxima color:Blue
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86 Use advanced settings?:No
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87 Threshold setting version:11
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88 Threshold strategy:Global
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89 Thresholding method:Minimum Cross-Entropy
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
90 Threshold smoothing scale:1.3488
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
91 Threshold correction factor:1.0
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
92 Lower and upper bounds on threshold:0.0,1.0
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
93 Manual threshold:0.0
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
94 Select the measurement to threshold with:None
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
95 Two-class or three-class thresholding?:Two classes
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
96 Assign pixels in the middle intensity class to the foreground or the background?:Foreground
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
97 Size of adaptive window:50
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
98 Lower outlier fraction:0.05
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
99 Upper outlier fraction:0.05
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
100 Averaging method:Mean
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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parents:
diff changeset
101 Variance method:Standard deviation
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
102 # of deviations:2.0
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
103 Thresholding method:Otsu
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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104
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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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]
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
106 Select the input image:PH3
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
107 Name the primary objects to be identified:PH3
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
108 Typical diameter of objects, in pixel units (Min,Max):7,80
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
109 Discard objects outside the diameter range?:Yes
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
110 Discard objects touching the border of the image?:Yes
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
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111 Method to distinguish clumped objects:Intensity
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
112 Method to draw dividing lines between clumped objects:Intensity
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
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diff changeset
113 Size of smoothing filter:10
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
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diff changeset
114 Suppress local maxima that are closer than this minimum allowed distance:7.0
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
115 Speed up by using lower-resolution image to find local maxima?:Yes
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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parents:
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116 Fill holes in identified objects?:After declumping only
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
117 Automatically calculate size of smoothing filter for declumping?:Yes
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
118 Automatically calculate minimum allowed distance between local maxima?:Yes
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
119 Handling of objects if excessive number of objects identified:Continue
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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120 Maximum number of objects:500
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
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121 Display accepted local maxima?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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parents:
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122 Select maxima color:Blue
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
123 Use advanced settings?:Yes
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
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124 Threshold setting version:11
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
125 Threshold strategy:Global
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
126 Thresholding method:Otsu
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
127 Threshold smoothing scale:1.3488
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
128 Threshold correction factor:1.0
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
129 Lower and upper bounds on threshold:0.0,1.0
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
130 Manual threshold:0.0
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
131 Select the measurement to threshold with:None
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
132 Two-class or three-class thresholding?:Three classes
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
133 Assign pixels in the middle intensity class to the foreground or the background?:Foreground
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
134 Size of adaptive window:50
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
135 Lower outlier fraction:0.05
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
136 Upper outlier fraction:0.05
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
137 Averaging method:Mean
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
138 Variance method:Standard deviation
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
139 # of deviations:2.0
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
140 Thresholding method:Otsu
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
141
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
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]
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
143 Parent objects:Nuclei
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
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diff changeset
144 Child objects:PH3
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
145 Calculate child-parent distances?:None
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
146 Calculate per-parent means for all child measurements?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
147 Calculate distances to other parents?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
148 Do you want to save the children with parents as a new object set?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
149 Name the output object:None
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
150 Parent name:None
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
151 Parent name:None
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
152
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
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]
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
154 Select the input objects:Nuclei
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
155 Name the objects to be identified:Cells
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
156 Select the method to identify the secondary objects:Propagation
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
157 Select the input image:cellbody
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
158 Number of pixels by which to expand the primary objects:10
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
159 Regularization factor:0.05
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
160 Discard secondary objects touching the border of the image?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
161 Discard the associated primary objects?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
162 Name the new primary objects:FilteredNuclei
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
163 Fill holes in identified objects?:Yes
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
164 Threshold setting version:11
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
165 Threshold strategy:Global
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
166 Thresholding method:Minimum Cross-Entropy
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
167 Threshold smoothing scale:0.0
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
168 Threshold correction factor:0.8
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
169 Lower and upper bounds on threshold:0.0,1.0
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
170 Manual threshold:0.0
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
171 Select the measurement to threshold with:None
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
172 Two-class or three-class thresholding?:Three classes
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
173 Assign pixels in the middle intensity class to the foreground or the background?:Foreground
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
174 Size of adaptive window:50
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
175 Lower outlier fraction:0.05
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
176 Upper outlier fraction:0.05
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
177 Averaging method:Mean
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
178 Variance method:Standard deviation
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
179 # of deviations:2.0
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
180 Thresholding method:Otsu
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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181
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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parents:
diff changeset
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]
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
bgruening
parents:
diff changeset
183 Select the larger identified objects:Cells
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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184 Select the smaller identified objects:Nuclei
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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185 Name the tertiary objects to be identified:Cytoplasm
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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186 Shrink smaller object prior to subtraction?:Yes
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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187
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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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]
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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189 Select images to measure:DNA, PH3
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
190 Select objects to measure:Nuclei, Cells, Cytoplasm
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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191
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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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]
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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193 Select object sets to measure:Nuclei, Cells, Cytoplasm
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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194 Calculate the Zernike features?:Yes
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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195 Calculate the advanced features?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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196
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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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]
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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198 Display outlines on a blank image?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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199 Select image on which to display outlines:DNA
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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200 Name the output image:OrigOverlay
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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201 Outline display mode:Color
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
202 Select method to determine brightness of outlines:Max of image
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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203 How to outline:Thick
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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204 Select outline color:#0080FF
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
205 Select objects to display:Cells
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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206 Select outline color:blue
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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207 Select objects to display:Nuclei
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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208 Select outline color:yellow
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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209 Select objects to display:PH3
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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210
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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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]
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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212 Select the type of image to save:Image
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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213 Select the image to save:OrigOverlay
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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214 Select method for constructing file names:From image filename
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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215 Select image name for file prefix:DNA
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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216 Enter single file name:OrigBlue
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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217 Number of digits:4
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
218 Append a suffix to the image file name?:Yes
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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219 Text to append to the image name:_Overlay
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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220 Saved file format:png
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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221 Output file location:Default Output Folder|
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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222 Image bit depth:8-bit integer
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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223 Overwrite existing files without warning?:Yes
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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224 When to save:Every cycle
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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225 Record the file and path information to the saved image?:Yes
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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226 Create subfolders in the output folder?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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227 Base image folder:Elsewhere...|
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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228 How to save the series:T (Time)
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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229
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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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]
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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231 Select the column delimiter:Comma (",")
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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232 Add image metadata columns to your object data file?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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233 Add image file and folder names to your object data file?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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234 Select the measurements to export:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
235 Calculate the per-image mean values for object measurements?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
236 Calculate the per-image median values for object measurements?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
237 Calculate the per-image standard deviation values for object measurements?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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238 Output file location:Default Output Folder|
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
239 Create a GenePattern GCT file?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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240 Select source of sample row name:Metadata
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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241 Select the image to use as the identifier:None
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
242 Select the metadata to use as the identifier:None
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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243 Export all measurement types?:Yes
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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244 Press button to select measurements:
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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245 Representation of Nan/Inf:NaN
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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246 Add a prefix to file names?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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247 Filename prefix:MyExpt_
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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248 Overwrite existing files without warning?:Yes
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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249 Data to export:Do not use
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
250 Combine these object measurements with those of the previous object?:No
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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251 File name:DATA.csv
b333df978624 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
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diff changeset
252 Use the object name for the file name?:Yes