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bio-imaging-mass-cytometry-phenotyping

维护者 FreedomIntelligence · 最近更新 2026年4月1日

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.

OpenClawNanoClaw分析处理复现实验bio-imaging-mass-cytometry-phenotyping🧬 bioinformatics (gptomics bio-* suite)bioinformatics — immunoinformatics & flow cytometrycell

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

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

维护者
FreedomIntelligence
许可
MIT
最近更新
2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

  • Python：scanpy.tl.leiden() ，用于 unsupervised 聚类，then manual annotation。
  • R：FlowSOM ，用于 self-organizing map-based phenotyping。
  • Assign cell types to my segmented IMC cells" → Classify cells based on protein marker expression ，使用 聚类，manual gating，或 supervised 分类 approaches. Python：scanpy.tl.leiden() ，用于 unsupervised 聚类，then manual annotation R：FlowSOM ，用于 self-organizing map-based phenotyping。
  • adata = ad.read_h5ad('imc_segmented.h5ad')。

原始文档

SKILL.md 摘录

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)

适用场景

  • 适合在assigning cell types to segmented IMC cells based on protein marker expression 或 when phenotyping cells in multiplexed imaging data时使用。

不适用场景

  • Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。

上游相关技能

  • 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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