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

Get started#

Install with Python >=3.8 and <3.11:

pip install bento-tools

Check out the documentation for the installation guide, tutorials, API and more! Read and cite our preprint if you use Bento in your work.

Main Features#

Bento Analysis Workflow
  • 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

GitHub license