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:10.1101/2023.01.28.525943

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

bioRxiv [Preprint]. 2023 Feb 23:2023.01.28.525943. doi: 10.1101/2023.01.28.525943.

Authors

Chaichontat Sriworarat¹, Annie Nguyen², Nicholas J Eagles², Leonardo Collado-Torres², Keri Martinowich^{1

2

3

4}, Kristen R Maynard^{1

2

3}, Stephanie C Hicks^{5

6}

Affiliations

¹ Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
² Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
³ Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.
⁴ The Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA.
⁵ Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
⁶ Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA.

Abstract

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.

Keywords: georeferencing; interactive image viewer; multi-dimensional image; single-cell transcriptomics; spatially-resolved transcriptomics; web-based browser.

Publication types

Preprint

Abstract

Publication types

Grants and funding