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

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 ima...

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Bibliographic Details
Published inBiological imaging (Cambridge, England) Vol. 3; p. e15
Main Authors Sriworarat, Chaichontat, Nguyen, Annie, Eagles, Nicholas J, Collado-Torres, Leonardo, Martinowich, Keri, Maynard, Kristen R, Hicks, Stephanie C
Format Journal Article
LanguageEnglish
Published England Cambridge University Press 2023
Subjects
Annotations
Cloud computing
Datasets
Gene expression
Genomics
georeferencing
interactive image viewer
Metadata
multi-dimensional image
single-cell transcriptomics
Software Report
spatially resolved transcriptomics
Transcriptomics
User interface
Visualization
Web browsers
web-based browser
Fiji
single-cell transcriptomics
georeferencing
multi-dimensional image
spatially resolved transcriptomics
interactive image viewer
web-based browser
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Summary: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.
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ISSN:2633-903X
2633-903X
DOI:10.1017/S2633903X2300017X