spatial-transcriptomics-spatial-data-io

Name: spatial-transcriptomics-spatial-data-io
Availability: InStock
Author: PharMolix

Load spatial transcriptomics platform outputs into unified AnnData or SpatialData objects.

1.1k|132|Updated Apr 13, 2023

Search Tags:#io #spatial-transcriptomics #anndata #xenium #spatialdata #visium #squidpy

Ready to run

npx skills add https://github.com/PharMolix/OpenBioMed --skill spatial-transcriptomics-spatial-data-io

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: spatial-transcriptomics-spatial-data-io
Source: https://github.com/PharMolix/OpenBioMed/tree/main/skills/spatial-transcriptomics-spatial-data-io
Command: npx skills add https://github.com/PharMolix/OpenBioMed --skill spatial-transcriptomics-spatial-data-io

SYSTEM DOCUMENTATION & REQUIREMENTS

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.

Frequently Asked Questions about spatial-transcriptomics-spatial-data-io

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

FAQPage Schema

How do I load Visium and Xenium spatial transcriptomics data into a unified format?▼

Loading Visium and Xenium spatial transcriptomics data into a unified format requires parsing platform-specific outputs to assemble standardized AnnData or SpatialData objects. This Skill identifies Space Ranger and Xenium outputs, extracting expression matrices, coordinates, and tissue images into a single structure.

Can I convert between SpatialData and AnnData objects while preserving spatial coordinates?▼

Converting between SpatialData and AnnData objects preserves spatial coordinates in obsm['spatial'] and images in uns['spatial']. This Skill maintains coordinates, tissue images, and platform-specific metadata across formats during the conversion process.

What spatial transcriptomics platforms are supported for standardized data loading?▼

Supported spatial transcriptomics platforms include Visium, Xenium, MERFISH, Slide-seq, CosMx, and Stereo-seq. The Skill identifies these platform-specific outputs and loads expression matrices, coordinates, and images into unified data objects.

Do I need squidpy and spatialdata to parse platform outputs into spatial data structures?▼

Parsing platform outputs into spatial data structures requires squidpy, spatialdata_io, spatialdata, scanpy, and anndata. These dependencies are necessary to assemble robust spatial data structures from diverse spatial transcriptomics platform outputs.

Why use a unified spatial data object for diverse platform outputs?▼

A unified spatial data object for diverse platform outputs enables seamless downstream analyses and immediate visualization. Standardizing outputs from platforms like Xenium and MERFISH into AnnData preserves tissue images and spatial coordinates in accessible fields.

Does loading Slide-seq and CosMx data preserve platform-specific metadata?▼

Loading Slide-seq and CosMx data preserves platform-specific metadata within the assembled SpatialData or AnnData representations. The Skill exposes spatial coordinates and tissue images while maintaining the original platform metadata across formats.