stLENS Tutorials

Welcome to the stLENS tutorials repository! This collection provides comprehensive guides and reproducible examples for using stLENS with spatial transcriptomics data.

Tutorial Overview

Getting Started

• Basic Tutorial - Introduction to stLENS fundamentals
  • Installation and setup
  • Basic usage with VisiumHD and STOmics data
  • Step-by-step workflow examples

Paper Reproduction

These tutorials reproduce the key analyses and figures from the stLENS paper:

• Spatial Analysis Tutorial - Reproduce spatial transcriptomics results

  • VisiumHD and STOmics data analysis
  • Spatial principal component optimization
  • Performance benchmarking
  • Figure generation for paper results

• Time Series Analysis - Reproduce temporal analysis benchmarks

  • Performance evaluation with different dataset sizes (10k, 30k, 50k, 100k, 500k, 1m cells)
  • Runtime comparison and scalability analysis

Prerequisites

Before running the tutorials, ensure you have:

• Python 3.9, 3.10, or 3.11
• CuPy for GPU acceleration (conda install cupy)
• stLENS installed (pip install stLENS)
• Jupyter Notebook or JupyterLab

Quick Start

1. Clone the repository:

   git clone https://github.com/pnucolab/stLENS-tutorials.git
   cd stLENS-tutorials

2. Install dependencies:

   conda install cupy
   pip install stLENS 

3. Start with the basic tutorial:

   jupyter notebook tutorial.ipynb

Related Documentation

• Main Documentation: https://stlens.readthedocs.io/
• API Reference: https://stlens.readthedocs.io/en/latest/api/index.html