spahdmap 0.1.5

Interpretable high-definition dimension reduction of spatial transcriptomics data by SpaHDmap

SpaHDmap: deep fusion of spatial transcriptomics and histology images for interpretable high-definition embedding mapping

Overview

SpaHDmap is based on a multi-modal neural network that takes advantage of the high-dimensionality of transcriptomics data and the high-definition of image data to achieve interpretable high-definition dimension reduction. The high-dimensional expression data enable refined functional annotations and the high-definition image data help to enhance the spatial resolution.

Based on the high-definition embedding and the reconstruction of gene expressions, SpaHDmap can then perform high-definition downstream analyses, such as spatial domain detection, gene expression recovery, and identification of embedding-associated genes as well as high-definition cluster-associated genes.

For more details, please refer to our manuscript.

Installation

Please install SpaHDmap from pypi with:

pip install SpaHDmap

Or clone this repository and use

pip install .

in the root of this repository.

Documentation

Please refer to the documentation for more details, for examples:

• to get the detailed information about installation, please refer to the installation guide.
• to get started with SpaHDmap, please refer to the tutorials.
• to download the example data, please refer to the Google Drive

License

This software package is licensed under MIT license. For commercial use, please contact Ruibin Xi.