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Imaging Biological Samples with Optical Microscopy01:18

Imaging Biological Samples with Optical Microscopy

Optical microscopy uses optic principles to provide detailed images of samples. Antonie van Leeuwenhoek designed the first compound optical microscope in the 17th century to visualize blood cells, bacteria, and yeast cells. In 1830, Joseph Jackson Lister created an essentially modern light microscope. The 20th century saw the development of microscopes with enhanced magnification and resolution.
In optical microscopy, the specimen to be viewed is placed on a glass slide and clipped on the stage...

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

Danni Luo1, Sophie Robertson2, Yuanchun Zhan1

  • 1Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-8821, USA.

Gigascience
|June 22, 2026
PubMed
Summary

ScopeViewer is a new browser-based software that simplifies visualizing complex spatial transcriptomics (ST) and pathology image data. It provides secure, high-resolution, and interactive exploration of molecular and image features.

Keywords:
Data privacyDigital pathologyGene expression profilingH&E stainingMASLDSpatial transcriptomicsTumor microenvironmentWeb-based visualization

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Medical Imaging

Background:

  • Spatial transcriptomics (ST) offers high-resolution molecular analysis within tissue contexts.
  • Visualizing large ST datasets with molecular information presents significant handling and sharing challenges.

Purpose of the Study:

  • To introduce ScopeViewer, a novel browser-based software solution.
  • To address the complexities of visualizing and sharing large-scale spatial transcriptomics and pathology image data.

Main Methods:

  • Developed a browser-based software application, ScopeViewer.
  • Implemented functionalities for visualizing large image data at multiple zoom levels.
  • Enabled dual interactive viewing of images and annotations.
  • Optimized bandwidth for displaying spatial molecular features.
  • Designed to circumvent data transfers for enhanced security.

Main Results:

  • ScopeViewer effectively visualizes large image data with annotations at various zoom levels.
  • Dual interactive viewing provides comprehensive contextual understanding.
  • Optimized bandwidth ensures a smooth user experience for spatial molecular features.
  • The software bolsters data security by avoiding direct data transfers.

Conclusions:

  • ScopeViewer provides a convenient, powerful, and secure platform for researchers.
  • It supports high-resolution image visualization, including pathology and spatial transcriptomics data.
  • The open-source platform encourages community contributions and future enhancements.