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数据与复现单细胞与空间组学FreedomIntelligence/OpenClaw-Medical-Skills数据与复现
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bio-spatial-transcriptomics-image-analysis

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

Process and analyze tissue images from spatial transcriptomics data using Squidpy. Extract image features, segment cells/nuclei, and compute morphological features from H&E or IF images. Use when processing tissue images for spatial transcriptomics.

OpenClawNanoClaw分析处理复现实验bio-spatial-transcriptomics-image-analysis🧬 bioinformatics (gptomics bio-* suite)bioinformatics — single-cell & spatial omicsprocess

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-spatial-transcriptomics-image-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.im.process()，squidpy.im.segment() ，支持 Cellpose backend。
  • Segment cells in my tissue image" → Extract image features，segment nuclei/cells，、 compute morphological features ，面向 H&E 或 immunofluorescence images paired ，支持 spatial data. Python：squidpy.im.process()，squidpy.im.segment() ，支持 Cellpose backend。
  • 提取 features 、 segment tissue images in spatial transcriptomics data。
  • 库_id = list(adata.uns['spatial'].keys())[0] img_dict = adata.uns['spatial'][库_id]['images']。

原始文档

SKILL.md 摘录

High and low resolution images

hires = img_dict['hires'] lowres = img_dict['lowres']

print(f'Hires shape: {hires.shape}') print(f'Lowres shape: {lowres.shape}')

Get scale factors

scalef = adata.uns['spatial'][library_id]['scalefactors'] spot_diameter = scalef['spot_diameter_fullres'] hires_scale = scalef['tissue_hires_scalef']


## Create ImageContainer

**Goal:** Wrap tissue images in Squidpy's ImageContainer for structured access and feature extraction.

**Approach:** Initialize an ImageContainer from the AnnData image data or a TIFF file.

```python

适用场景

  • 适合在processing tissue images ，用于 spatial transcriptomics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

  • spatial-data-io - Load spatial data with images
  • spatial-visualization - Visualize images with expression
  • spatial-domains - Use image features for domain detection

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