Mercurial > repos > bgruening > cp_relate_objects
view test-data/measure_image_quality.cppipe @ 5:3a3033222f61 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
author | bgruening |
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date | Fri, 26 Feb 2021 14:20:37 +0000 |
parents | f3f45c42bc36 |
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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.\'\x5D|batch_state:array(\x5B\x5D, 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.\'\x5D|batch_state:array(\x5B\x5D, 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 MeasureImageQuality:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False] Calculate metrics for which images?:All loaded images Image count:1 Scale count:1 Threshold count:1 Select the images to measure: Include the image rescaling value?:Yes Calculate blur metrics?:Yes Spatial scale for blur measurements:20 Calculate saturation metrics?:Yes Calculate intensity metrics?:Yes Calculate thresholds?:Yes Use all thresholding methods?:No Select a thresholding method:Otsu Typical fraction of the image covered by objects:0.1 Two-class or three-class thresholding?:Two classes Minimize the weighted variance or the entropy:Weighted variance Assign pixels in the middle intensity class to the foreground or the background?:Foreground