STIM

STIM provides a comprehensive computational pipeline for the integration and analysis of spatial transcriptomics data. This tool is designed to integrate tissue histology with both high-definition spatial transcriptomics (e.g., Xenium) and transcriptome-wide spatial transcriptomics (e.g., Visium). STIM enables:

• Mapping gene expression across different spatial transcriptomics platforms
• Analyzing cell neighborhoods to identify spatial patterns and interactions
• Inferring ligand-receptor interactions

Installation

Installation using pip:
pip install pySTIM

Import

import pySTIM as pst

Usage

• Cross-Modality Integration of Single-Cell Resolution Xenium In Situ Data and Whole Transcriptome Visium Data
• Cell Neighborhoods Mapping and Functional Characterization
• Inference of Ligand-Receptor Interactions
• Core Visualization Functions