spatial-transcriptomics-spatial-data-io
CommunityUnified spatial data I/O for diverse platforms.
AuthorPharMolix
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms into standardized AnnData/SpatialData objects for seamless downstream analyses.
Core Features & Use Cases
- Load platform-specific outputs (Space Ranger Visium, Xenium, MERFISH, Slide-seq, CosMx, Stereo-seq) into unified data structures.
- Preserve and expose spatial coordinates in obsm['spatial'] and images/scale factors in uns['spatial'], enabling immediate visualization.
- Convert between SpatialData and AnnData representations, maintaining coordinates, images, and metadata across formats.
Quick Start
Load Visium Space Ranger output to create a standardized AnnData object with spatial coordinates and tissue images.
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: spatial-transcriptomics-spatial-data-io Download link: https://github.com/PharMolix/OpenBioMed/archive/main.zip#spatial-transcriptomics-spatial-data-io Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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