AN
Data & Repro
AnnData
AnnData is a Python package for handling annotated data matrices, storing experimental measurements (X) alongside observation metadata (obs)…
K-Dense-AI/claude-scientific-skillsView
Data & Repro
BI
bio-spatial-transcriptomics-image-analysis
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-spatial-transcriptomics-image-analysis
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Python: squidpy.im.process(), squidpy.im.segment() with Cellpose backend.
- Segment cells in my tissue image" → Extract image features, segment nuclei/cells, and compute morphological features from H&E or immunofluorescence images paired with spatial data. Python: squidpy.im.process(), squidpy.im.segment() with Cellpose backend.
- Extract features and segment tissue images in spatial transcriptomics data.
- library_id = list(adata.uns['spatial'].keys())[0] img_dict = adata.uns['spatial'][library_id]['images'].
Source Doc
Excerpt From SKILL.md
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
Use cases
- Use when processing tissue images for spatial transcriptomics.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- 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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