bio-imaging-mass-cytometry-data-preprocessing - IMC Data Preprocessing
Load and preprocess IMC and MIBI data files
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
- estimate spillover matrix
- normalize images
- transform images
- process batch images
- create AnnData objects
- visualize images
Inputs
- MCD files
- panel file
- spillover matrix
- single-stain controls
- Ilastik classifier
Outputs
- TIFF images
- filtered images
- corrected images
- normalized images
- probability maps
- AnnData files
Requirements
- Python environment
- anndata 0.10+
- numpy 1.26+
- pandas 2.2+
- scanpy 1.10+
- scipy 1.12+
- steinbock 0.16+
- readimc
- napari