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bio-imaging-mass-cytometry-spatial-analysis

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

bio-imaging-mass-cytometry-spatial-analysis：Spatial analysis of cell neighborhoods 、 interactions in IMC data。 Covers neighbor graphs，spatial statistics，、 interaction testing。 适合在analyzing spatial relationships between cell types，testing ，用于 neighborhood enrichment，或 identifying cell-cell interaction patterns in imaging mass cytometry data时使用。

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

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

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

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：squidpy.gr.spatial_neighbors()，squidpy.gr.nhood_enrichment()。
  • 分析 spatial cell interactions in my IMC data" → Build spatial neighborhood graphs，test ，用于 cell-cell interaction enrichment，、 identify spatial domains ，面向 multiplexed imaging data. Python：squidpy.gr.spatial_neighbors()，squidpy.gr.nhood_enrichment()。
  • adata = ad.read_h5ad('imc_phenotyped.h5ad')。

原始文档

SKILL.md 摘录

Build Spatial Graph

import squidpy as sq
import anndata as ad

## Build spatial neighbor graph

sq.gr.spatial_neighbors(adata, coord_type='generic', delaunay=True)

## Or by distance

sq.gr.spatial_neighbors(adata, coord_type='generic', radius=50)  # 50 pixels

print(f'Built graph with {adata.obsp["spatial_connectivities"].nnz} edges')

适用场景

  • 适合在analyzing spatial relationships between cell types，testing ，用于 neighborhood enrichment，或 identifying cell-cell interaction patterns in imaging mass cytometry 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

  • phenotyping - Assign cell types first
  • spatial-transcriptomics/spatial-statistics - Similar spatial methods
  • single-cell/cell-communication - Interaction concepts

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