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数据与复现
BI
bio-spatial-transcriptomics-spatial-data-io
维护者 FreedomIntelligence · 最近更新 2026年4月1日
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.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-spatial-transcriptomics-spatial-data-io
- 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
核心说明
- 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 ，支持 spatial coordinates 、 tissue images. Python：squidpy.read.visium('spaceranger_out/')，spatialdata.read_zarr()。
- Load 、 work ，支持 spatial transcriptomics data ，面向 various 平台s。
- adata = sq.read.visium('path/to/spaceranger/output/') print(f'Loaded {adata.n_obs} spots，{adata.n_vars} genes')。
原始文档
SKILL.md 摘录
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}')
适用场景
- 适合在loading Visium，Xenium，MERFISH，或 other spatial 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
- 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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