bio-spatial-transcriptomics-spatial-proteomics
Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization. Use when working with multiplexed imaging data, analyzing protein spatial patterns, or integrating spatial proteomics with transcriptomics.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-spatial-transcriptomics-spatial-proteomics --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: anndata 0.10+, 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 Proteomics Analysis **"Analyze my CODEX/IMC spatial proteomics data"** → Process multiplexed imaging data including cell segmentation, protein phenotyping, spatial neighborhood analysis, and protein colocalization scoring. - Python: `scimap.tl.phenotype_cells()`, `squidpy.gr.nhood_enrichment()` ## Data Loading **Goal:** Process multiplexed spatial proteomics data (CODEX/IMC/MIBI) through cell phenotyping, spatial neighborhood analysis, and protein colocalization scoring. **Approach:** Load the cell-by-marker intensity matrix with spatial coordinates into AnnData, normalize and rescale marker intensities, phenotype cells by marker expression gating, then analyze spatial neighborhoods and cell-cell interactions using scimap and squidpy. ```python import scimap as
- Version Compatibility
- Data Loading
- Preprocessing
- Phenotyping Cells
- Spatial Analysis
- Visualization
- Integration with Transcriptomics
- Platform-Specific Notes
- Related Skills
What does the bio-spatial-transcriptomics-spatial-proteomics skill do?
Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization. Use when working with multiplexed imaging data, analyzing protein spatial patterns, or integrating spatial proteomics with transcriptomics.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-spatial-transcriptomics-spatial-proteomics --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.