# 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](https://www.biorxiv.org/content/10.1101/2024.09.12.612666).
## Installation
Please install `SpaHDmap` from pypi with:
```bash
pip install SpaHDmap
```
Or clone this repository and use
```bash
pip install .
```
in the root of this repository.
## Documentation
Please refer to the [documentation](https://spahdmap.readthedocs.io/en/latest/) for more details, for examples:
- to get the detailed information about installation, please refer to the [installation guide](https://spahdmap.readthedocs.io/en/latest/installation.html).
- to get started with SpaHDmap, please refer to the [tutorials](https://spahdmap.readthedocs.io/en/latest/tutorials/index.html).
- to download the example data, please refer to the [Google Drive](https://drive.google.com/drive/folders/16L1nm3TzDDTFPVAaRXVKRp4LuCqvXbt2)
## License
This software package is licensed under MIT license. For commercial use, please contact [Ruibin Xi](ruibinxi@math.pku.edu.cn).
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