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

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.

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.

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.