bio-spatial-transcriptomics-spatial-visualization
Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and annotations overlaid on histology images. Use when visualizing spatial expression patterns.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-spatial-transcriptomics-spatial-visualization --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: matplotlib 3.8+, numpy 1.26+, scanpy 1.10+, squidpy 1.3+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Spatial Visualization **"Plot gene expression on my tissue section"** → Overlay gene expression, cluster assignments, or continuous scores on spatial coordinates with optional histology image background. - Python: `squidpy.pl.spatial_scatter(adata, color='gene')`, `scanpy.pl.spatial(adata, color='leiden')` Create visualizations for spatial transcriptomics data. ## Required Imports ```python import squidpy as sq import scanpy as sc import matplotlib.pyplot as plt ``` ## Basic Spatial Plot **Goal:** Create a spatial scatter plot with spots colored by a variable of interest. **Approach:** Use Squidpy's `spatial_scatter` to overlay expression or metadata values on tissue coordinates. ```python # Plot spots colored by a variable sq.pl.spatial_scatter(adata, c
- Version Compatibility
- Required Imports
- Basic Spatial Plot
- Plot with Scanpy
- Show Tissue Image
- Customize Appearance
- Gene Expression on Tissue
- Expression with Colorbar Control
- Compare Conditions/Samples
- Overlay Annotations
- Co-expression Plot
- Visualize Spatial Statistics
- Interactive Visualization with Napari
- Save Publication-Quality Figures
What does the bio-spatial-transcriptomics-spatial-visualization skill do?
Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and annotations overlaid on histology images. Use when visualizing spatial expression patterns.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-spatial-transcriptomics-spatial-visualization --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.