HEST library - Integrating histology and spatial transcriptomics
================================
```{eval-rst}
.. image:: https://img.shields.io/github/stars/mahmoodlab/HEST?style=social
   :target: https://github.com/mahmoodlab/HEST
   :alt: GitHub Stars

.. image:: https://img.shields.io/badge/NeurIPS-2024-blue.svg
    :target: https://proceedings.neurips.cc/paper_files/paper/2024/file/60a899cc31f763be0bde781a75e04458-Paper-Datasets_and_Benchmarks_Track.pdf
    :alt: NeurIPS 2024

.. toctree::
   :maxdepth: 3
   :hidden:

   installation
   api
   tutorials
```



`hest` is a Python library for the preprocessing and registration of H&E and Spatial Transcriptomics pairs. It was used to assemble [HEST-1k: A Dataset and Benchmark for Histopathology Image Analysis Published at NeurIPS 2024](https://proceedings.neurips.cc/paper_files/paper/2024/file/60a899cc31f763be0bde781a75e04458-Paper-Datasets_and_Benchmarks_Track.pdf).

For the documentations of core WSI manipulations methods please visit the [hestcore documentation](https://hestcore.readthedocs.io/en/latest/) (work in progress).

```{eval-rst}
.. card:: Installation
    :link: installation
    :link-type: doc

    Installation instructions for ``hest``.

.. card:: API
    :link: api
    :link-type: doc

    API documentation of ``hest``.

.. card:: Tutorials
    :link: tutorials
    :link-type: doc

    Concrete examples on how to use ``hest``.
```

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<img src=_static/joint_logo.png>