view test-data/measure_image_quality.cppipe @ 5:d0178bdcd00e draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
author bgruening
date Fri, 26 Feb 2021 14:12:26 +0000
parents 72a7f23f3a79
children
line wrap: on
line source

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