Data & ReproSingle-Cell & Spatial OmicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-spatial-transcriptomics-spatial-multiomics

Maintainer FreedomIntelligence · Last updated April 1, 2026

Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular resolution or high-density spatial data.

OpenClawNanoClawAnalysisReproductionbio-spatial-transcriptomics-spatial-multiomics🧬 bioinformatics (gptomics bio-* suite)bioinformatics — single-cell & spatial omicsanalyze

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Python: spatialdata + squidpy for unified multi-platform analysis.
Analyze my high-resolution spatial data" → Process subcellular-resolution spatial platforms (Xenium, MERFISH, Slide-seq, Stereo-seq) including cell segmentation, binning strategies, and multi-modal integration. Python: spatialdata + squidpy for unified multi-platform analysis.
adata = sc.read_h5ad('spatial_multiomics.h5ad').

Source Doc

Excerpt From SKILL.md

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')

Use cases

Use when working with subcellular resolution or high-density spatial data.

Not for

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

Upstream Related Skills

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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