Bento: a toolkit for subcellular analysis of spatial transcriptomics data

Clarence K Mah; Noorsher Ahmed; Nicole A Lopez; Dylan C Lam; Avery Pong; Alexander Monell; Colin Kern; Yuanyuan Han; Gino Prasad; Anthony J Cesnik; Emma Lundberg; Quan Zhu; Hannah Carter; Gene W Yeo

doi:10.1186/s13059-024-03217-7

Bento: a toolkit for subcellular analysis of spatial transcriptomics data

Genome Biol. 2024 Apr 2;25(1):82. doi: 10.1186/s13059-024-03217-7.

Authors

Clarence K Mah^#^{1

2

3}, Noorsher Ahmed^#^{2

3}, Nicole A Lopez², Dylan C Lam^{2

3

4}, Avery Pong², Alexander Monell^{2

5}, Colin Kern⁶, Yuanyuan Han⁶, Gino Prasad^{2

5}, Anthony J Cesnik⁷, Emma Lundberg^{7

8

9}, Quan Zhu⁶, Hannah Carter¹, Gene W Yeo^{10

11

12

13}

Affiliations

¹ Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
² Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
³ Sanford Stem Cell Institute Innovation Center, La Jolla, CA, USA.
⁴ Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
⁵ Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
⁶ Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
⁷ Department of Bioengineering, Stanford University, Stanford, CA, USA.
⁸ Department of Pathology, Stanford University, Stanford, CA, USA.
⁹ Chan-Zuckerberg Biohub, San Francisco, CA, USA.
¹⁰ Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA. geneyeo@ucsd.edu.
¹¹ Sanford Stem Cell Institute Innovation Center, La Jolla, CA, USA. geneyeo@ucsd.edu.
¹² Stem Cell Program, University of California San Diego, La Jolla, CA, USA. geneyeo@ucsd.edu.
¹³ Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA. geneyeo@ucsd.edu.

^# Contributed equally.

PMID: 38566187
DOI: 10.1186/s13059-024-03217-7

Abstract

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.

MeSH terms

Cell Communication
Ecosystem*
Gene Expression Profiling
Propanolamines*
Single-Cell Analysis
Transcriptome

Substances

befunolol
Propanolamines

Abstract

MeSH terms

Substances

Grants and funding