Welcome to SpatialTis’s documentation!

SpatialTis is an ultra-fast spatial analysis toolkit for large-scale spatial single-cell data.

• ✔️ Spatial Transcriptome (Non single-cell)

• ✔️ Spatial Proteome (Single-cell)

• 🦀 Core algorithms implements in Rust

• 🚀 Parallel processing support

🔋 Highlighted spatial analysis

• Cell neighbors search (KD-Tree/R-Tree/Delaunay)

• Cell-Cell Interaction

• Marker spatial co-expression

• Spatial variable genes (current support: SOMDE)

• GCNG: Inferring ligand-receptor using graph convolution network

• Identify neighbor dependent markers

📦 Other analysis

• Spatial distribution

• Hotspot detection

• Spatial auto-correlation

• Spatial heterogeneity

For a quick view of what it’s does, check our the tutorial part.

• User Guide
  • Installation
  • Getting Started
  • Input Data
  • Multiplexed images to AnnData
  • Read Visium Result Folders to AnnData
  • Low-Level API

• API Reference
  • Config
  • Cell quantification from Images
  • Read from 10x visium
  • WKT Format helper
  • IO
  • Basic analysis
  • Spatial analysis
  • Base class
  • ROI Visualization
  • Analysis Visualization

• Examples
  • IMC diabetes dataset, 1.8 Million cells

• About
  • Implementation
  • Development Guide
  • Q&A