Darwin Imcyto

Full analysis pipeline for Imaging Mass Cytometry data: segmentation, cell phenotyping, and spatial analysis Steps: Step 1: MCD File Preprocessing; Step 2: Ilastik Probability Maps; Step 3: Cell Segmentation (DeepCell); Step 4: CellProfiler Quantification; Step 5: Cell Phenotyping (Scanpy); Step 6: Spatial Neighbourhood Analysis; Step 7: IMCyto Report. Verticals: spatial_omics, immunogenomics.

Use in DarwinOmics

How to use it

Use this workflow element when the submitted analysis needs a multi-step execution path, imported workflow, Darwinomics wrapper, or workflow-scale comparison rather than a single module.