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Related Experiment Video

Updated: Apr 30, 2026

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

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

Chaichontat Sriworarat¹, Annie Nguyen², Nicholas J Eagles²

¹Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.

Biological Imaging

|March 15, 2024

Summary

This summary is machine-generated.

Samui is a new web-based tool for visualizing large biological images quickly. It allows researchers to easily share, explore, and annotate complex imaging data, accelerating scientific discovery.

Keywords:

georeferencing interactive image viewer multi-dimensional image single-cell transcriptomics spatially resolved transcriptomics web-based browser

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Last Updated: Apr 30, 2026

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Published on: March 5, 2022

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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

Area of Science:

Biology
Bioinformatics
Computational Biology

Background:

High-resolution and multiplexed imaging generate large, complex multidimensional datasets.
Visualizing and sharing these large biological images presents significant challenges for researchers.
Existing tools may lack the performance and interactivity needed for efficient exploration.

Purpose of the Study:

To introduce Samui, a novel, performant, and interactive web-based image visualization tool.
To enable fast visualization and annotation of large multidimensional biological images.
To facilitate seamless sharing and exploration of complex imaging data.

Main Methods:

Development of a web browser-based application, Samui.
Implementation of efficient algorithms for fast image rendering and data handling.
Testing with datasets from Vizgen MERFISH and 10x Genomics Visium Spatial Gene Expression platforms.

Main Results:

Samui provides rapid visualization of large multidimensional images directly in the web browser.
Users can browse through extensive image datasets and specific features within seconds.
The tool supports interactive annotation, enhancing data exploration capabilities.

Conclusions:

Samui addresses the critical challenge of visualizing and sharing large-scale biological imaging data.
Its performance and accessibility accelerate the analysis and interpretation of complex spatial omics datasets.
The tool is readily available for use with example datasets.