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annotate test-data/display_data_on_image.cppipe @ 2:443638c10c61 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sun, 05 Nov 2023 09:31:03 +0000
parents 878bafb411dd
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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33bf7aa4e684 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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1 CellProfiler Pipeline: http://www.cellprofiler.org
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2 Version:3
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3 DateRevision:319
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4 GitHash:
33bf7aa4e684 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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5 ModuleCount:5
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6 HasImagePlaneDetails:False
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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]
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9 :
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10 Filter images?:Images only
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11 Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
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12
1
878bafb411dd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
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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]
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33bf7aa4e684 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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14 Extract metadata?:Yes
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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<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
33bf7aa4e684 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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21 Regular expression to extract from folder name:(?P<folderField1>.*)
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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:
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25 Match file and image metadata:[]
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26 Use case insensitive matching?:No
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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]
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29 Assign a name to:Images matching rules
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30 Select the image type:Grayscale image
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31 Name to assign these images:DNA
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32 Match metadata:[]
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33 Image set matching method:Order
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34 Set intensity range from:Image metadata
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35 Assignments count:1
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36 Single images count:0
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37 Maximum intensity:255.0
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38 Process as 3D?:No
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39 Relative pixel spacing in X:1.0
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40 Relative pixel spacing in Y:1.0
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41 Relative pixel spacing in Z:1.0
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42 Select the rule criteria:and (file does startwith "im")
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43 Name to assign these images:DNA
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44 Name to assign these objects:Cell
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45 Select the image type:Grayscale image
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46 Set intensity range from:Image metadata
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47 Select the image type:Grayscale image
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48 Maximum intensity:255.0
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49
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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]
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51 Do you want to group your images?:Yes
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52 grouping metadata count:1
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53 Metadata category:field1
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54
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55 DisplayDataOnImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\'Add nuclei id as label\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
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56 Display object or image measurements?:Object
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57 Select the input objects:Nuclei
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58 Measurement to display:Number_Object_Number
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59 Select the image on which to display the measurements:DNA
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60 Text color:#ff0000
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61 Name the output image that has the measurements displayed:ImageDisplay
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62 Font size (points):11
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63 Number of decimals:0
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64 Image elements to save:Image
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65 Annotation offset (in pixels):0
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66 Display mode:Text
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67 Color map:Default
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68 Display background image?:Yes
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69 Color map scale:Use this image's measurement range
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70 Color map range:0.0,1.0