domains / families / science / imc-pipeline

imc-pipeline

separate

Orchestrates imaging mass cytometry from raw MCD acquisitions to patient-level spatial analysis, chaining steinbock preprocessing, Mesmer/Cellpose segmentation, single-cell quantification, phenotyping, and squidpy spatial statistics. Use when committing the panel + segmentation frame + pixel size (every per-cell number is a mask-bounded pixel average), compensating channel spillover on PIXELS before segmentation but running REDSEA lateral-spillover on the per-cell table AFTER segmentation, using arcsinh cofactor 1 (not the suspension-CyTOF 5), and aggregating to the PATIENT before any cross-condition test (cells and ROIs from one patient are not independent replicates). Hands mechanism to the imaging-mass-cytometry component skills; not a re-teach of any single step.

When to use

• imaging mass cytometry pipeline orchestration
• raw MCD to spatial analysis
• steinbock preprocessing
• Mesmer/Cellpose segmentation
• single-cell quantification
• phenotyping
• squidpy spatial statistics
• patient-level aggregation

When not to use

• re-teaching any single step
• suspension-CyTOF analysis
• cell-level or per-image independent replicate testing

Skill page

Source