Welcome to the COSIE documentation!

COSIE enables within- and CrOss-subject Spatial multimodal Integration, prediction, and Enhancement.

To get started with cosie, check out the installation guide and tutorials.

Contents:

• Installation Guide
  • Installation
  • Dependencies
• Tutorials
  • Tutorial - Image feature extraction
  • Tutorial 1 - Periodontal data (Visium HD + CODEX)
  • Tutorial 2 - Atherosclerosis (Xenium + CODEX)
  • Tutorial 3 - Mouse brain (Spatial MALDI-Visium)
  • Tutorial 4 - Mouse hippocampus (Spatial MALDI-Visium)
  • Tutorial 5 - Mouse embryo (Spatial Mux-seq)
  • Tutorial 6 - Gastric cancer (Visium + COMET)
  • Tutorial 7 - Lung cancer (10x Visium Spatial Gene and Protein)
  • Tutorial 8 - Mouse spleen (SPOTS)
  • Tutorial 9 - LUAD TCGA integration
  • Tutorial 10 - B cell lymphoma (CosMx + CODEX)
  • Tutorial 11 - Tonsil (10x Visium Spatial Gene and Protein)
• API documentation
  • COSIE
• References

Citation

If you use this tool in your research, please cite our work.