Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-imaging-mass-cytometry-data-preprocessing

Maintainer FreedomIntelligence · Last updated April 1, 2026

Load and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image normalization. Use when starting IMC analysis from raw MCD files or preparing images for segmentation.

OpenClawNanoClawAnalysisReproductionbio-imaging-mass-cytometry-data-preprocessing🧬 bioinformatics (gptomics bio-* suite)bioinformatics — immunoinformatics & flow cytometryload

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-imaging-mass-cytometry-data-preprocessing

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: steinbock preprocess for automated IMC preprocessing pipeline.
Preprocess my imaging mass cytometry data" → Load MCD files, apply hot pixel removal, channel cropping, and signal normalization to prepare multiplexed images for segmentation and analysis. CLI: steinbock preprocess for automated IMC preprocessing pipeline.
steinbock preprocess imc \ --mcd raw/*.mcd \ --panel panel.csv \ -o img.

Source Doc

Excerpt From SKILL.md

panel.csv

channel,name,keep,ilastik 1,DNA1,1,1 2,CD45,1,1 3,CD3,1,0 4,CD8,1,0 5,CD4,1,0


## Python-Based Loading

```python
import readimc
import numpy as np
from pathlib import Path

## Read MCD file

mcd_file = Path('acquisition.mcd')
with readimc.MCDFile(mcd_file) as mcd:
    # List acquisitions
    for acquisition in mcd.acquisitions:
        print(f'Acquisition: {acquisition.id}')
        print(f'  Channels: {len(acquisition.channel_metals)}')
        print(f'  Size: {acquisition.width} x {acquisition.height}')

    # Load specific acquisition
    acq = mcd.acquisitions[0]
    img = mcd.read_acquisition(acq)  # Returns (C, H, W) array

    # Channel names
    channel_names = acq.channel_names