Mercurial > repos > bgruening > cp_save_images
diff test-data/gray_to_color.cppipe @ 3:a45d360ae9d9 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
author | bgruening |
---|---|
date | Mon, 11 May 2020 07:51:22 -0400 |
parents | |
children | 33f4fa1413fb |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gray_to_color.cppipe Mon May 11 07:51:22 2020 -0400 @@ -0,0 +1,75 @@ +CellProfiler Pipeline: http://www.cellprofiler.org +Version:3 +DateRevision:319 +GitHash: +ModuleCount:5 +HasImagePlaneDetails:False + +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] + : + Filter images?:Images only + Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".") + +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] + Extract metadata?:Yes + Metadata data type:Text + Metadata types:{} + Extraction method count:1 + Metadata extraction method:Extract from file/folder names + Metadata source:File name + 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]+) + Regular expression to extract from folder name:(?P<folderField1>.*) + Extract metadata from:All images + Select the filtering criteria:and (file does contain "") + Metadata file location: + Match file and image metadata:[] + Use case insensitive matching?:No + +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] + Assign a name to:Images matching rules + Select the image type:Grayscale image + Name to assign these images:DNA + Match metadata:[] + Image set matching method:Order + Set intensity range from:Image metadata + Assignments count:1 + Single images count:0 + Maximum intensity:255.0 + Process as 3D?:No + Relative pixel spacing in X:1.0 + Relative pixel spacing in Y:1.0 + Relative pixel spacing in Z:1.0 + Select the rule criteria:and (file does startwith "im") + Name to assign these images:DNA + Name to assign these objects:Cell + Select the image type:Grayscale image + Set intensity range from:Image metadata + Select the image type:Grayscale image + Maximum intensity:255.0 + +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] + Do you want to group your images?:Yes + grouping metadata count:1 + Metadata category:field1 + +GrayToColor:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\'Combine masks nuclei + nucleoli with colors\'\x5D|batch_state:array(\x5B], dtype=uint8)|enabled:True|wants_pause:False] + Select a color scheme:RGB + Select the image to be colored red:MaskNucleoli + Select the image to be colored green:Leave this black + Select the image to be colored blue:MaskNuclei + Name the output image:CombinedMask + Relative weight for the red image:0.8 + Relative weight for the green image:1.0 + Relative weight for the blue image:0.5 + Select the image to be colored cyan:Leave this black + Select the image to be colored magenta:Leave this black + Select the image to be colored yellow:Leave this black + Select the image that determines brightness:Leave this black + Relative weight for the cyan image:1.0 + Relative weight for the magenta image:1.0 + Relative weight for the yellow image:1.0 + Relative weight for the brightness image:1.0 + Hidden:1 + Image name:None + Color:#FF0000 + Weight:1.0