skills/bioskills/bio-imaging-mass-cytometry-data-preprocessing/scripts/preprocess_imc.py

• remove_hot_pixels · function · L13-L23 — def remove_hot_pixels(img, threshold=50): # 8-neighbor maximum; a pixel exceeding every neighbor by > threshold (an absolute # COUNT difference, not a universal constant -- raise for high-dynamic-range markers) # is a spike and is replaced by the neighbor max. Valleys are never filled, so real # bright edges and sparse single-positive pixels survive.
• arcsinh_cofactor1 · function · L25-L28 — def arcsinh_cofactor1(cell_means): # cofactor 1 for IMC single-cell means (Hunter 2024 Cytometry A 105:36); the # suspension-CyTOF cofactor 5 over-compresses IMC's lower-count cell means
• zscore_cohort · function · L30-L33 — def zscore_cohort(expr, cohort_mean, cohort_std): # z-score against COHORT-WIDE statistics, not per-image, so scales stay comparable # across samples; per-image scaling destroys cross-sample comparability