Cell Painting and other pipelines from the Imaging Platform.
Note:
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Each pipeline has two versions – one with
CreateBatchFilesmodule enabled (named e.g.analysis.cppipe), and the other with the moduled disabled (named e.g.analysis_without_batchfile.cppipe). When updating the pipeline, ensure that these two versions are always in sync. The former is required by a script for creating CellProfiler batch files, which in turn are used to create a list of groups of images to be processed together, as well as Distributed-CellProfiler configuration files. The latter is used to run the pipeline using Distributed-CellProfiler. -
The
ExportToSpreadsheetmodule should always be configured with these values in order that the files are saved in a standard format and location
Select the column delimiter:Comma (",")
Add image metadata columns to your object data file?:No
Limit output to a size that is allowed in Excel?:No
Select the measurements to export:No
Output file location:Default Output Folder\x7C
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
:
Representation of Nan/Inf:NaN
Add a prefix to file names?:No
Filename prefix:
Overwrite existing files without warning?:Yes
Data to export:Do not use
Combine these object measurements with those of the previous object?:No
File name:
Use the object name for the file name?:Yes
- The
SaveImagesmodule should always be configured with these values in order that the files are saved in a standard format and location. The values shown forSelect image name for file prefixandEnter single file nameare specific for this example and should be adapted appropriately.
Select image name for file prefix:OrigDNA
Enter single file name:\\\\g<Well>_s\\\\g<Site>--nuclei_outlines
Output file location:Default Output Folder sub-folder\x7Coutlines
Overwrite existing files without warning?:Yes