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数据与复现
BI
bio-spatial-transcriptomics-spatial-multiomics
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular resolution or high-density spatial data.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-spatial-transcriptomics-spatial-multiomics
- 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：spatialdata + squidpy ，用于 unified multi-平台 analysis。
- 分析 my high-resolution spatial data" → Process subcellular-resolution spatial 平台s (Xenium，MERFISH，Slide-seq，Stereo-seq) ，涵盖 cell 分割，binning strategies，、 multi-modal integration. Python：spatialdata + squidpy ，用于 unified multi-平台 analysis。
- adata = sc.read_h5ad('spatial_multiomics.h5ad')。
原始文档
SKILL.md 摘录
Platform Comparison
| Platform | Resolution | Spots/Beads | Coverage |
|---|---|---|---|
| Visium | 55 µm | ~5,000 | Tissue-wide |
| Visium HD | 2 µm | ~11M | Subcellular |
| Slide-seq | 10 µm | ~100,000 | High-density |
| Stereo-seq | 0.5 µm | >200M | Subcellular |
| MERFISH | Single-molecule | N/A | Targeted genes |
Squidpy for High-Resolution Data
Goal: Run standard spatial analyses (autocorrelation, neighborhood enrichment, ligand-receptor) on high-resolution spatial data.
Approach: Adjust neighbor graph density for high-resolution platforms, then apply standard Squidpy workflows.
import squidpy as sq
import scanpy as sc
## Spatial neighbors (for high-resolution, adjust n_neighs based on density)
sq.gr.spatial_neighbors(adata, coord_type='generic', n_neighs=10, spatial_key='spatial')
适用场景
- 适合在working ，支持 subcellular resolution 或 high-density 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-transcriptomics/spatial-preprocessing - Standard spatial analysis
- single-cell/preprocessing - scRNA-seq concepts
- spatial-transcriptomics/image-analysis - Morphology processing
- single-cell/cell-annotation - Cell type assignment
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