Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments

Chaichontat Sriworarat; Annie Nguyen; Nicholas J. Eagles; Leonardo Collado-Torres; Keri Martinowich; Kristen R. Maynard; Stephanie C. Hicks

doi:10.1017/S2633903X2300017X

Biological Imaging (Jan 2023)

Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments

Chaichontat Sriworarat,
Annie Nguyen,
Nicholas J. Eagles,
Leonardo Collado-Torres,
Keri Martinowich,
Kristen R. Maynard,
Stephanie C. Hicks

Affiliations

Chaichontat Sriworarat: ORCiD; Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
Annie Nguyen: ORCiD; Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
Nicholas J. Eagles: ORCiD; Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
Leonardo Collado-Torres: ORCiD; Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
Keri Martinowich: ORCiD; Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA The Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA
Kristen R. Maynard: ORCiD; Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
Stephanie C. Hicks: ORCiD; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA

DOI: https://doi.org/10.1017/S2633903X2300017X
Journal volume & issue: Vol. 3

Abstract

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High-resolution and multiplexed imaging techniques are giving us an increasingly detailed observation of a biological system. However, sharing, exploring, and customizing the visualization of large multidimensional images can be a challenge. Here, we introduce Samui, a performant and interactive image visualization tool that runs completely in the web browser. Samui is specifically designed for fast image visualization and annotation and enables users to browse through large images and their selected features within seconds of receiving a link. We demonstrate the broad utility of Samui with images generated with two platforms: Vizgen MERFISH and 10x Genomics Visium Spatial Gene Expression. Samui along with example datasets is available at https://samuibrowser.com.

Published in Biological Imaging

ISSN: 2633-903X (Online)
Publisher: Cambridge University Press
Country of publisher: United Kingdom
LCC subjects: Science: Biology (General); Medicine: Medicine (General): Medical technology
Website: https://www.cambridge.org/core/journals/biological-imaging

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Abstract

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