Processing pipeline

• Pipeline overview
  • Dataset structure
  • Pipeline scheme

• Pipeline steps
  • Image acquisition
  • Initial processing
    • Create directories
    • Create configuration files
  • Filtering, raw counting and Stitching
  • Consolidate experiment
  • Transfer the stitched files and data
  • Register the stitched images
  • Create the stitched images for all genes
  • Dots coords processing
  • Staining segmentation
  • Counting dots in segmented regions

• Scripts
  • Add coords to Experimental_metadata.yaml config file
  • Process standalone experiment
  • Preprocessing
  • Reference channel registration
  • Apply stitching to osmFISH channels
  • Staining segmentation
  • Dots coords correction

• Configuration files
  • Experimental metadata
  • Filtering and raw counting
  • Staining segmentation
  • Coordinate file: