bio-spatial-transcriptomics-pyxa-starmap
OfficialLoad Pyxa STARmap data into AnnData.
Authorstellaromics
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Load Pyxa STARmap spatial transcriptomics data into a unified AnnData object, preserving 3D coordinates, segmentation, and FOV metadata for downstream analysis.
Core Features & Use Cases
- Version-aware loading: handles versioned outputs (cell_by_gene, cell_metadata, cell_assigned_gene, segmentation_geometries) and preserves ROI- and AG-level schemas.
- 3D spatial context: captures X_um, Y_um, Z_um and volumetric metadata (Volume_um3) for robust spatial analyses.
- Quality metadata & controls: preserves FOV structure and negative controls (blank genes, ERCC spike-ins) for accurate downstream normalization.
- Use Case: researchers loading Pyxa STARmap outputs into AnnData to perform integrated spatial analyses with Scanpy/Squidpy.
Quick Start
Provide the path to your STARmap/Pyxa output directory to load the data into an AnnData object.
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: bio-spatial-transcriptomics-pyxa-starmap Download link: https://github.com/stellaromics/fast-bioinfo/archive/main.zip#bio-spatial-transcriptomics-pyxa-starmap Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
Agent Skills Search Helper
Install a tiny helper to your Agent, search and equip skill from 471,000+ vetted skills library on demand.