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Broad Imaging Platform pipelines

Cell Painting and other pipelines from the Imaging Platform.

Guidelines for creating pipelines

Note:

  1. Each pipeline has two versions – one with CreateBatchFiles module 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.

  2. The ExportToSpreadsheet module 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
  1. The SaveImages module should always be configured with these values in order that the files are saved in a standard format and location. The values shown for Select image name for file prefix and Enter single file name are 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