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bio-spatial-transcriptomics-spatial-data-io

Maintainer FreedomIntelligence · Last updated April 1, 2026

Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData. Read Space Ranger outputs, convert formats, and access spatial coordinates. Use when loading Visium, Xenium, MERFISH, or other spatial data.

OpenClawNanoClawAnalysisReproductionbio-spatial-transcriptomics-spatial-data-io🧬 bioinformatics (gptomics bio-* suite)bioinformatics — single-cell & spatial omicsload

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-spatial-transcriptomics-spatial-data-io

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Python: squidpy.read.visium('spaceranger_out/'), spatialdata.read_zarr().
  • Load my Visium spatial data" → Read spatial transcriptomics outputs (Visium, Xenium, MERFISH, Slide-seq) into AnnData objects with spatial coordinates and tissue images. Python: squidpy.read.visium('spaceranger_out/'), spatialdata.read_zarr().
  • Load and work with spatial transcriptomics data from various platforms.
  • adata = sq.read.visium('path/to/spaceranger/output/') print(f'Loaded {adata.n_obs} spots, {adata.n_vars} genes').

Source Doc

Excerpt From SKILL.md

Load 10X Visium Data

Goal: Load Visium spatial transcriptomics data from Space Ranger output into an AnnData object.

Approach: Use Squidpy's read.visium to parse the output directory, which loads expression, spatial coordinates, and tissue images.


## Spatial coordinates are in adata.obsm['spatial']

print(f"Spatial coords shape: {adata.obsm['spatial'].shape}")

## Image is in adata.uns['spatial']

library_id = list(adata.uns['spatial'].keys())[0]
print(f'Library ID: {library_id}')

Use cases

  • Use when loading Visium, Xenium, MERFISH, or other spatial data.

Not for

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

Upstream Related Skills

  • spatial-preprocessing - QC and normalization after loading
  • spatial-visualization - Plot spatial data
  • single-cell/data-io - Non-spatial scRNA-seq data loading

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