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Bento: a toolkit for subcellular analysis of spatial transcriptomics data.

Clarence K MahNoorsher AhmedNicole A LopezDylan C LamAvery PongAlexander MonellColin KernYuanyuan HanGino PrasadAnthony J CesnikEmma LundbergQuan ZhuHannah CarterGene W Yeo
Published in: Genome biology (2024)
The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell-cell interactions, and spatial expression patterns, they are limited to the multicellular scale. We present Bento, a Python toolkit that takes advantage of single-molecule information to enable spatial analysis at the subcellular scale. Bento ingests molecular coordinates and segmentation boundaries to perform three analyses: defining subcellular domains, annotating localization patterns, and quantifying gene-gene colocalization. We demonstrate MERFISH, seqFISH + , Molecular Cartography, and Xenium datasets. Bento is part of the open-source Scverse ecosystem, enabling integration with other single-cell analysis tools.
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