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5.7.6. Overview Workflow

The following is the overview workflow for the image correction processing itself. This does not include the wrappers that go along with the code for the AstroPath Pipeline.

Input Parameters: <base>, <FWpath>, <SlideID>

  • fixM2: Make sure that the _M2.im3 files are properly resolved. Remove the original, and rename the _M2
    • Input
      • <base>
      • <SlideID>
  • ShredDat: Extract parameters from the Im3s
    • Input
      • <base>
      • <FW_path>
      • <SlideID>
    • Output
      • a full XML extraction of the first .im3 file (.full.im3)
        • <SlideID>.full.xml
        • Into <FW_path>\<SlideID>
      • Extract the ‘shape’ and ‘magnification’
        • <SlideID>.Parameters.xml
      • Loop through all the .im3 images and extract SpectralBasisInfo.Exposure.Protocol.DarkCurrentSettings.xml (.SpectralBasisInfo.Exposure.Protocol.DarkCurrentSettings.xml)
        • Into <FW_path>\<SlideID>
        • <filename>.SpectralBasisInfo.Exposure.Protocol.DarkCurrentSettings.xml for each .im3
      • Loop through all the .im3 images and extract the binary data (.DATA.dat)
        • into a <FW_path>\<SlideID>
        • <filename>.Data.dat for each .im3 image
  • ApplyCorr: Apply the flat field and warping (.fw)
    • Input
      • <FW_path>
      • <SlideID>
    • Output:
      • in the <FW_path>\<SlideID>
      • <filename>.fw for each .im3 image
        • the bitmap image in single column format
  • InjectDat: Re-insert binary data into the .im3 files
    • Input
      • <base>
      • <FW_path>
      • <SlideID>
    • Output:
      • into <base>\<SlideID>\<flatw_im3_path>
      • corrected <filename>.im3 for each .im3 image
  • ExtractLayer: Extract the DAPI layer from .fw files. We extract the first layer with an .fw01 extension
    • Input
      • <FW_path>
      • <SlideID>
    • Output
      • in the <FW_path>\<SlideID>
      • <filename>.fw01 for each .im3 image
        • the bitmap image in single column format for the first layer (DAPI)
  • cleanup: Clean up the path
    • Input
      • <FW_path>
      • <SlideID>
    • Output
      • Delete .DATA.dat files but keep .fw, .fw01, and .SpectralBasisInfo.Exposure.Protocol.DarkCurrentSettings.xml and send them to a <base>\<SlideID>\<xml_path> directory