SubDomain

subdomain allows identification of domains from segmentation-free analysis of spatially-resolved transcriptomics. More generally it can be applied to any labeled 2D grid data.

Installation

subdomain can currently be installed from GitHub via

pip install git+https://github.com/HiDiHlabs/SubDomain.git

For detailed installation instructions please refer to the documentation.

Documentation

For documentation of the package please refer to GitHub pages.

Citations

tbd

ToDo

• Reduce dependencies by using a jax-based
  • GMM library (e.g. https://github.com/adonath/gmmx ?); allows dropping pytorch dependencies
  • K-means library (e.g. https://github.com/YosefLab/scib-metrics ?); allows dropping cupy dependencies
• Test benefits of GPU acceleration. Currently likely memory constrained. Switch to CPU-only clustering?

License

This project is licensed under the MIT License - for details please refer to the LICENSE file.