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sc_extraction_pipeline.cppipe
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sc_extraction_pipeline.cppipe
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CellProfiler Pipeline: http://www.cellprofiler.org
Version:5
DateRevision:424
GitHash:
ModuleCount:9
HasImagePlaneDetails:False
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]
:
Filter images?:Images only
Select the rule criteria:and (extension does isimage) (directory doesnot containregexp "[\\\\/]\\.")
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]
Extract metadata?:No
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<Plate>.*)_(?P<Well>[A-P][0-9]{2})_s(?P<Site>[0-9])_w(?P<ChannelNumber>[0-9])
Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
Extract metadata from:All images
Select the filtering criteria:and (file does contain "")
Metadata file location:Elsewhere...|
Match file and image metadata:[]
Use case insensitive matching?:No
Metadata file name:None
Does cached metadata exist?:No
NamesAndTypes:[module_num:3|svn_version:'Unknown'|variable_revision_number:8|show_window:False|notes:['The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Assign a name to:All images
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 contain "")
Name to assign these images:DNA
Name to assign these objects:Cell
Select the image type:Grayscale image
Set intensity range from:Image metadata
Maximum intensity:255.0
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]
Do you want to group your images?:No
grouping metadata count:1
Metadata category:None
ConvertImageToObjects:[module_num:5|svn_version:'Unknown'|variable_revision_number:1|show_window:True|notes:['This module converts the segmentation mask image into individual objects.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Select the input image:DNA
Name the output object:ConvertImageToObjects
Convert to boolean image:No
Preserve original labels:Yes
Background label:0
Connectivity:0
FilterObjects:[module_num:6|svn_version:'Unknown'|variable_revision_number:10|show_window:True|notes:['The module filters objects (cells) which are adjoining to the image borders.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Select the objects to filter:ConvertImageToObjects
Name the output objects:FilterObjectsBorder
Select the filtering mode:Image or mask border
Select the filtering method:Limits
Select the objects that contain the filtered objects:None
Select the location of the rules or classifier file:Elsewhere...|
Rules or classifier file name:rules.txt
Class number:1
Measurement count:1
Additional object count:0
Assign overlapping child to:Both parents
Keep removed objects as a separate set?:No
Name the objects removed by the filter:RemovedObjects
Select the measurement to filter by:AreaShape_Area
Filter using a minimum measurement value?:Yes
Minimum value:0.0
Filter using a maximum measurement value?:Yes
Maximum value:1.0
Allow fuzzy feature matching?:No
MeasureObjectIntensityMultichannel:[module_num:7|svn_version:'Unknown'|variable_revision_number:4|show_window:True|notes:['This module extract the intensities of each cell for all selected images/channels. Make sure to select FilterObjectsBorder as the objects to measure.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Select images to measure:DNA
Select objects to measure:FilterObjectsBorder
How many channels does the image have?:1
MeasureObjectSizeShape:[module_num:8|svn_version:'Unknown'|variable_revision_number:3|show_window:True|notes:['This module extract the size and shape of each cell. Make sure to select FilterObjectsBorder as the objects to measure.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Select object sets to measure:FilterObjectsBorder
Calculate the Zernike features?:Yes
Calculate the advanced features?:No
ExportToSpreadsheet:[module_num:9|svn_version:'Unknown'|variable_revision_number:13|show_window:True|notes:["This module exports all measured single cell features. Make sure to select the relevant measurements by clicking the button 'Press button to select measurements' and choosing which measurements to export."]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Select the column delimiter:Comma (",")
Add image metadata columns to your object data file?:No
Add image file and folder names to your object data file?:No
Select the measurements to export:Yes
Calculate the per-image mean values for object measurements?:No
Calculate the per-image median values for object measurements?:No
Calculate the per-image standard deviation values for object measurements?:No
Output file location:Default Output Folder|
Create a GenePattern GCT file?:No
Select source of sample row name:Metadata
Select the image to use as the identifier:None
Select the metadata to use as the identifier:None
Export all measurement types?:Yes
Press button to select measurements:
Representation of Nan/Inf:NaN
Add a prefix to file names?:Yes
Filename prefix:SC_DATA
Overwrite existing files without warning?:No
Data to export:Do not use
Combine these object measurements with those of the previous object?:No
File name:DATA.csv
Use the object name for the file name?:Yes