bio-spatial-transcriptomics-spatial-data-io
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-spatial-transcriptomics-spatial-data-io --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+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, spatialdata 0.1+, 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 Data I/O **"Load my Visium spatial data"** → Read spatial transcriptomics outputs (Visium, Xenium, MERFISH, Slide-seq) into AnnData objects with spatial coordinates and tissue images. - Python: `squidpy.read.visium('spaceranger_out/')`, `spatialdata.read_zarr()` Load and work with spatial transcriptomics data from various platforms. ## Required Imports ```python import squidpy as sq import scanpy as sc import anndata as ad import spatialdata as sd import spatialdata_io as sdio ``` ## 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,
- Version Compatibility
- Required Imports
- Load 10X Visium Data
- Load Visium with Scanpy
- Load 10X Xenium Data
- Load with SpatialData (Recommended for New Projects)
- Load MERFISH Data
- Load Slide-seq Data
- Load Nanostring CosMx
- Load Stereo-seq Data
- Load from H5AD with Spatial Coordinates
- Create Spatial AnnData from Scratch
- Access Spatial Coordinates
- Access Tissue Images
What does the bio-spatial-transcriptomics-spatial-data-io skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-spatial-transcriptomics-spatial-data-io --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.