bio-imaging-mass-cytometry-data-preprocessing - IMC Data Preprocessing
Load and preprocess imaging mass cytometry data using steinbock and Python for hot pixel removal and image normalization.
Tags
Updated: 2026-03-26Capabilities
Typical Inputs
Typical Outputs
What this skill does
- load MCD files
- convert MCD to TIFF
- remove hot pixels
- apply spillover correction
- normalize images
- transform data
Inputs
- MCD files
- panel CSV files
- spillover matrix files
- Ilastik project files
Outputs
- TIFF images
- probability maps
- normalized images
Requirements
- Python 3.x
- steinbock 0.16+
- anndata 0.10+
- numpy 1.26+
- pandas 2.2+
- scanpy 1.10+
- scipy 1.12+