Interactive Histology of large-scale biomedical image stacks

Won Ki Jeong*, Jens Schneider, Stephen Turney, Beverly E. Faulkner-Jones, Dominik Meyer, Rüdiger Westermann, R. Clay Reid, Jeff Lichtman, Hanspeter Pfister

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

27 Scopus citations


Histology is the study of the structure of biological tissue using microscopy techniques. As digital imaging technology advances, high resolution microscopy of large tissue volumes is becoming feasible; however, new interactive tools are needed to explore and analyze the enormous datasets. In this paper we present a visualization framework that specifically targets interactive examination of arbitrarily large image stacks. Our framework is built upon two core techniques: display-aware processing and GPU-accelerated texture compression. With display-aware processing, only the currently visible image tiles are fetched and aligned on-the-fly, reducing memory bandwidth and minimizing the need for time-consuming global pre-processing. Our novel texture compression scheme for GPUs is tailored for quick browsing of image stacks. We evaluate the usability of our viewer for two histology applications: digital pathology and visualization of neural structure at nanoscale-resolution in serial electron micrographs.

Original languageEnglish (US)
Article number5613479
Pages (from-to)1386-1395
Number of pages10
JournalIEEE Transactions on Visualization and Computer Graphics
Issue number6
StatePublished - 2010

Bibliographical note

Funding Information:
This work was supported in part by the National Science Foundation under Grant No. PHY-0835713, the National Institutes of Health under Grant No. 1P30NS062685-01 and R01 NS020364-23, The Gatsby Charitable Foundation under Grant GAT3036-Connectomic Consortium, and through generous support from Microsoft Research and NVIDIA. We wish to thank Dr. Su-Jean Seo for participating in the user study.


  • GPU
  • Gigapixel viewer
  • biomedical image processing
  • texture compression

ASJC Scopus subject areas

  • Software
  • Signal Processing
  • Computer Vision and Pattern Recognition
  • Computer Graphics and Computer-Aided Design


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