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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Detalles Bibliográficos
Autores principales: Sriworarat, Chaichontat, Nguyen, Annie, Eagles, Nicholas J., Collado-Torres, Leonardo, Martinowich, Keri, Maynard, Kristen R., Hicks, Stephanie C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9900917/
https://www.ncbi.nlm.nih.gov/pubmed/36747726
http://dx.doi.org/10.1101/2023.01.28.525943
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author Sriworarat, Chaichontat
Nguyen, Annie
Eagles, Nicholas J.
Collado-Torres, Leonardo
Martinowich, Keri
Maynard, Kristen R.
Hicks, Stephanie C.
author_facet Sriworarat, Chaichontat
Nguyen, Annie
Eagles, Nicholas J.
Collado-Torres, Leonardo
Martinowich, Keri
Maynard, Kristen R.
Hicks, Stephanie C.
author_sort Sriworarat, Chaichontat
collection PubMed
description 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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spelling pubmed-99009172023-02-07 Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments Sriworarat, Chaichontat Nguyen, Annie Eagles, Nicholas J. Collado-Torres, Leonardo Martinowich, Keri Maynard, Kristen R. Hicks, Stephanie C. bioRxiv Article 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. Cold Spring Harbor Laboratory 2023-02-23 /pmc/articles/PMC9900917/ /pubmed/36747726 http://dx.doi.org/10.1101/2023.01.28.525943 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Sriworarat, Chaichontat
Nguyen, Annie
Eagles, Nicholas J.
Collado-Torres, Leonardo
Martinowich, Keri
Maynard, Kristen R.
Hicks, Stephanie C.
Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments
title Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments
title_full Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments
title_fullStr Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments
title_full_unstemmed Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments
title_short Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments
title_sort performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9900917/
https://www.ncbi.nlm.nih.gov/pubmed/36747726
http://dx.doi.org/10.1101/2023.01.28.525943
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