general worfklow / data pipeline

🚧 WIP 🚧

PUTATIVE WORKFLOW

WORKFLOW EDITOR PLUGIN

• FINE-TUNE SEGMENTATIONS
• export workflow.jsons
  • masks:
  • nuclei
  • cellmask
  • cytoplasm
  • organelles:
  • lyso
  • mito
  • golgi
  • perox
  • ER
  • LD

BATCHPROCESS WORKFLOW

• BATCH PROCESS
• load workflow.jsons for:
• masks
  • export: masks .tiff as stack (nuclei, cellmask, cytoplasm)
• organelles
  • export individual .tiffs

NOTEBOOK ~~OR FUTURE PLUGIN~~

• COLLECT ORGANELLE STATS
• extract masks.tiffs as individual
  • nuclei, cellmask, cytoplasm
• collect regionprops for all organelles
  • export .csvs

---