Data & ReproProtein Structure & DesignFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-imaging-mass-cytometry-phenotyping

Maintainer FreedomIntelligence · Last updated April 1, 2026

Cell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification approaches. Use when assigning cell types to segmented IMC cells based on protein marker expression or when phenotyping cells in multiplexed imaging data.

OpenClawNanoClawAnalysisReproductionbio-imaging-mass-cytometry-phenotyping🧬 bioinformatics (gptomics bio-* suite)bioinformatics — immunoinformatics & flow cytometrycell

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Python: scanpy.tl.leiden() for unsupervised clustering, then manual annotation.
R: FlowSOM for self-organizing map-based phenotyping.
Assign cell types to my segmented IMC cells" → Classify cells based on protein marker expression using clustering, manual gating, or supervised classification approaches. Python: scanpy.tl.leiden() for unsupervised clustering, then manual annotation R: FlowSOM for self-organizing map-based phenotyping.
adata = ad.read_h5ad('imc_segmented.h5ad').

Source Doc

Excerpt From SKILL.md

Load Single-Cell Data

import anndata as ad
import scanpy as sc
import pandas as pd
import numpy as np

## Or create from CSVs

intensities = pd.read_csv('cell_intensities.csv')
cell_info = pd.read_csv('cell_info.csv')

adata = ad.AnnData(X=intensities.values)
adata.var_names = intensities.columns
adata.obs = cell_info

Arcsinh transformation (standard for cytometry)

def arcsinh_transform(adata, cofactor=5): adata.X = np.arcsinh(adata.X / cofactor) return adata

adata = arcsinh_transform(adata)

Use cases

Use when assigning cell types to segmented IMC cells based on protein marker expression or when phenotyping cells in multiplexed imaging data.

Not for

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

Upstream Related Skills

cell-segmentation - Generate single-cell data
spatial-analysis - Analyze spatial patterns of cell types
single-cell/cell-annotation - Similar annotation concepts

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