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bio-spatial-transcriptomics-pyxa-starmap

Loads Pyxa STARmap spatial transcriptomics data into AnnData objects with 3D coordinates and metadata.

Updated Aug 23, 2026
Search Tags:#segmentation#starmap#spatial-transcriptomics#anndata#scanpy#pyxa#fov
One-click install
npx skills add https://github.com/stellaromics/fast-bioinfo --skill bio-spatial-transcriptomics-pyxa-starmap
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-spatial-transcriptomics-pyxa-starmap
Source: https://github.com/stellaromics/fast-bioinfo/tree/main/.claude/agents/spatial-analysis/skills/bio-spatial-transcriptomics-pyxa-starmap
Command: npx skills add https://github.com/stellaromics/fast-bioinfo --skill bio-spatial-transcriptomics-pyxa-starmap

SYSTEM DOCUMENTATION & REQUIREMENTS

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.

Frequently Asked Questions about bio-spatial-transcriptomics-pyxa-starmap

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I load Pyxa STARmap spatial transcriptomics data into an AnnData object?▼

The loader preserves negative controls like blank genes and ERCC spike-ins during spatial transcriptomics data import, keeping them accessible in the AnnData object to support accurate downstream normalization and quality control.

Does this STARmap loader support 3D coordinates and volumetric metadata?▼

Yes, the loader captures X_um, Y_um, Z_um coordinates and volumetric metadata like Volume_um3, ensuring the AnnData object retains full 3D spatial context for robust downstream spatial analyses.

Can I use the loaded AnnData object with Scanpy and Squidpy for downstream analysis?▼

Yes, the loader handles ROI-level and AG-level schemas, preserving FOV structure and segmentation geometries so your spatial transcriptomics data maintains its organizational hierarchy in the AnnData object.

What should I do if my STARmap output has a different versioned schema?▼

The loader is version-aware and handles various versioned outputs including cell_by_gene, cell_metadata, and cell_assigned_gene, but you should verify your library versions and adjust API usage if compatibility issues arise.

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