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Spatial Data I/O - Usage Guide

Overview

This skill covers loading spatial transcriptomics data from various platforms including 10X Visium, Xenium, MERFISH, Slide-seq, and more using Squidpy and SpatialData.

Prerequisites

pip install squidpy spatialdata spatialdata-io scanpy anndata

Quick Start

Tell your AI agent what you want to do:

  • "Load my Visium data from the Space Ranger output"
  • "Read this Xenium experiment"
  • "Load my MERFISH spatial data"

Example Prompts

Visium

"Load my 10X Visium data"

"Read the Space Ranger output in this folder"

Xenium

"Load my Xenium data"

"Read single-cell spatial data from Xenium"

Other Platforms

"Load my MERFISH data"

"Read Slide-seq bead coordinates"

"Import CosMx data"

What the Agent Will Do

  1. Identify the appropriate reader for your platform
  2. Load expression data into AnnData format
  3. Extract spatial coordinates
  4. Load tissue images if available
  5. Return a properly formatted spatial object

Tips

  • Visium uses spots (~55um), while Xenium/MERFISH have single-cell resolution
  • SpatialData is the newer format that handles multi-modal spatial data well
  • Library ID is needed to access images in Visium data
  • Coordinates are stored in adata.obsm['spatial'] as (x, y) pairs