bio-imaging-mass-cytometry-data-preprocessing - IMC Data Preprocessing
Preprocess imaging mass cytometry (IMC) data from MCD files with hot pixel removal and 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
- estimate spillover matrix
- normalize images
- apply arcsinh transform
- create AnnData objects
- process batch images
- generate probability maps
- visualize images
Inputs
- MCD files
- panel CSV file
- spillover matrix CSV
- Ilastik classifier project
Outputs
- TIFF images
- preprocessed image arrays
- probability maps
- AnnData files
- napari visualizations
Requirements
- Python
- steinbock
- readimc
- numpy
- scipy
- pandas
- anndata
- tifffile
- napari