ScopeViewer: a browser-based solution for visualizing large biological images.

IF 5 2区生物学 Q1 MULTIDISCIPLINARY SCIENCES

GigaScience Pub Date : 2026-01-21 DOI:10.1093/gigascience/giag074

Danni Luo, Sophie Robertson, Yuanchun Zhan, Ruichen Rong, Shidan Wang, Xi Jiang, Sen Yang, Suzette Palmer, Peiran Quan, Hiroaki Kanzaki, Yujin Hoshida, Liwei Jia, Qiwei Li, Guanghua Xiao, Xiaowei Zhan

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引用次数: 0

Abstract

Background: Spatial transcriptomics (ST) enables a high-resolution interrogation of molecular characteristics within specific spatial contexts and tissue morphology. Despite its potential, visualization of ST data is a challenging task due to the complexities in handling, sharing, and visualizing large image datasets together with molecular information.

Results: We introduce ScopeViewer, a browser-based software designed to overcome these challenges. ScopeViewer offers the following functionalities: (1) it visualizes large image data and associated annotations at various zoom levels, allowing for intricate exploration of the data; (2) it enables dual interactive viewing of the original images along with their annotations, providing a comprehensive understanding of the context; (3) it displays spatial molecular features with optimized bandwidth, ensuring a smooth user experience; and (4) it bolsters data security by circumventing data transfers.

Conclusions and discussions: ScopeViewer offers the research community a convenient, powerful, and secure software for high-resolution images, including pathology images and ST. It serves as an open-source platform for imaging-based research. Future enhancements and new features will be shared on GitHub by the creators and are open for contributions from other researchers. ScopeViewer is freely available on the website at https://cdc.biohpc.swmed.edu/scopeviewer.

查看原文本刊更多论文

ScopeViewer：用于可视化大型生物图像的基于浏览器的解决方案。

背景：空间转录组学（ST）能够在特定的空间背景和组织形态中对分子特征进行高分辨率的询问。尽管具有潜力，但由于处理、共享和可视化大型图像数据集以及分子信息的复杂性，ST数据的可视化是一项具有挑战性的任务。结果：我们介绍了ScopeViewer，一个基于浏览器的软件，旨在克服这些挑战。ScopeViewer提供以下功能：(1)它以各种缩放级别可视化大型图像数据和相关注释，允许对数据进行复杂的探索；(2)它可以对原始图像及其注释进行双重交互查看，提供对上下文的全面理解；(3)空间分子特征展示，带宽优化，用户体验流畅；(4)它通过规避数据传输来增强数据安全性。结论和讨论：ScopeViewer为研究社区提供了一个方便、强大和安全的高分辨率图像软件，包括病理图像和空间转录组学。它是基于成像的研究的开源平台。未来的增强功能和新功能将由创建者在GitHub上共享，并向其他研究人员开放。ScopeViewer可在以下网站免费获得：https://cdc.biohpc.swmed.edu/scopeviewer。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

GigaScience MULTIDISCIPLINARY SCIENCES-

CiteScore

15.50

自引率

1.10%

发文量

119

审稿时长

1 weeks

期刊介绍： GigaScience seeks to transform data dissemination and utilization in the life and biomedical sciences. As an online open-access open-data journal, it specializes in publishing "big-data" studies encompassing various fields. Its scope includes not only "omic" type data and the fields of high-throughput biology currently serviced by large public repositories, but also the growing range of more difficult-to-access data, such as imaging, neuroscience, ecology, cohort data, systems biology and other new types of large-scale shareable data.