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bio-workflows-imc-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

Imaging mass cytometry: segmentation → phenotyping → spatial analysis.

OpenClawNanoClawAnalysisReproductionbio-workflows-imc-pipeline🧠 bioos extended suitebioos extended bioinformatics suiteimaging

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-workflows-imc-pipeline

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

steinbock preprocess imc \ --mcd data/*.mcd \ --panel panel.csv \ --output raw/.
steinbock preprocess imc hotpixel \ --input raw/ \ --output img/ \ --threshold 50.

Source Doc

Excerpt From SKILL.md

Create nuclear and membrane channels

steinbock preprocess mosaic
--input img/
--channels panel.csv
--output mosaics/


## Using Cellpose

steinbock segment cellpose \
    --input img/ \
    --panel panel.csv \
    --channel DNA1 DNA2 \
    --output masks/ \
    --diameter 20

## Alternative: Using Mesmer

steinbock segment mesmer \
    --input img/ \
    --panel panel.csv \
    --nuclear DNA1 DNA2 \
    --membrane CD45 \
    --output masks/

Use cases

Use bio-workflows-imc-pipeline for GIS and remote-sensing workflows.
Apply bio-workflows-imc-pipeline to earth observation and spatial analysis tasks.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

imaging-mass-cytometry/data-preprocessing - Hot pixel, spillover
imaging-mass-cytometry/cell-segmentation - Cellpose/Mesmer details
imaging-mass-cytometry/phenotyping - Cluster annotation
imaging-mass-cytometry/spatial-analysis - Spatial statistics
imaging-mass-cytometry/interactive-annotation - Manual cell labeling
imaging-mass-cytometry/quality-metrics - QC metrics

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