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# Bento

Bento is a Python toolkit for performing subcellular analysis of spatial transcriptomics data.

# Get started
Install with Python >=3.8 and <3.11:
```bash
pip install bento-tools
```

Check out the [documentation](https://bento-tools.readthedocs.io/en/latest/) for the installation guide, tutorials, API and more! Read and cite [our preprint](https://doi.org/10.1101/2022.06.10.495510) if you use Bento in your work.


# Main Features

<img src="_static/tutorial_img/bento_workflow.png" alt="Bento Analysis Workflow" width=800>


- Store molecular coordinates and segmentation masks
- Visualize spatial transcriptomics data at subcellular resolution
- Compute subcellular spatial features
- Predict localization patterns and signatures
- Factor decomposition for high-dimensional spatial feature sets

---
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```{toctree}
:maxdepth: 1
:hidden: true
   
installation
tutorials
api
howitworks
```