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Batch Effect Correction

Remove technical variation while preserving biological effects.

Technical Effects Modeled​

  • Donor effects
  • Imaging color
  • Imaging cycle

Biological Effects Preserved​

  • Marker effects
  • Region effects
  • Marker-region interactions

CLI​

celltype-refinery preprocess batch \
  --input aligned/ \
  --mode residual \
  --out output/corrected