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bio-imaging-mass-cytometry-data-preprocessing - IMC Data Preprocessing

Load and preprocess IMC and MIBI data with hot pixel removal and normalization

Tags

Updated: 2026-03-26
imaging mass cytometryIMCMIBIdata preprocessingimage processingspatial proteomics

Capabilities

load MCD filesconvert MCD to TIFFremove hot pixelsapply spillover correction

Typical Inputs

MCD filespanel CSV filespillover matrix

Typical Outputs

TIFF imagesfiltered imagesnormalized images

What this skill does

  • load MCD files
  • convert MCD to TIFF
  • remove hot pixels
  • apply spillover correction
  • normalize image data
  • estimate spillover matrix
  • create AnnData objects
  • visualize images
  • process batches

Inputs

  • MCD files
  • panel CSV file
  • spillover matrix
  • ilastik project

Outputs

  • TIFF images
  • filtered images
  • normalized images
  • probability maps
  • AnnData files

Requirements

  • Python 3.x
  • steinbock 0.16+
  • anndata 0.10+
  • numpy 1.26+
  • pandas 2.2+
  • scanpy 1.10+
  • scipy 1.12+
  • readimc
  • napari
  • tifffile

Source

  • Spec: SKILL.md

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