bio-imaging-mass-cytometry-data-preprocessing - IMC Data Preprocessing Pipeline
Load and preprocess imaging mass cytometry (IMC) data with MCD/TIFF handling, hot pixel removal, and normalization
Tags
Updated: 2026-03-26Capabilities
Typical Inputs
Typical Outputs
What this skill does
- load MCD files
- remove hot pixels
- crop channels
- normalize images
- convert MCD to TIFF
- apply spillover correction
- estimate spillover matrix
- apply arcsinh transformation
- create AnnData object
- process batch images
Inputs
- MCD files
- panel CSV file
- spillover matrix
- Ilastik classifier
Outputs
- TIFF images
- probability maps
- AnnData object
- processed images
Requirements
- Python 3.8+
- steinbock
- readimc
- Ilastik
- anndata