SpatialTis

Huge update will be happen at v0.3.0, API break, change data storage, plotting will isolate static and interactive plotting.

SpatialTis is a high-performance spatial analysis toolkit for single-cell multiplexed tissue data using AnnData object as input with parallel processing support.

Documentation:

Tutorial:

• MIBI Data (Breast cancer, 180K cells) | Download data
• IMC Data (Diabetes, 1.7M cells) | Download data

Download the examples and try it on your own, see how fast SpatialTis is.

Installation

pypi

Install the basics

pip install spatialtis

For the full features

pip install 'spatialtis[all]'

Install the current development version

pip install git+https://github.com/Mr-Milk/SpatialTis.git

SpatialTis modules

• Preprocessing
• Data statistic
  • Cell components
  • Cell density
  • Cell morphology
  • Cell co-occurrence
• Find cell neighbors
• Spatial analysis
  • Spatial distribution
  • Spatial heterogeneity
  • Hotspot detection
  • Cell-cell interaction
  • Markers co-expression
  • Spatial community detection
  • Neighbor dependent markers