An interactive visualization tool for multi-channel confocal microscopy data in neurobiology research

Yong Wan, H. Otsuna, Chi-Bin Chien, C. Hansen

Research output: Contribution to journalArticlepeer-review

64 Scopus citations

Abstract

Confocal microscopy is widely used in neurobiology for studying the three-dimensional structure of the nervous system. Confocal image data are often multi-channel, with each channel resulting from a different fluorescent dye or fluorescent protein; one channel may have dense data, while another has sparse; and there are often structures at several spatial scales: subneuronal domains, neurons, and large groups of neurons (brain regions). Even qualitative analysis can therefore require visualization using techniques and parameters fine-tuned to a particular dataset. Despite the plethora of volume rendering techniques that have been available for many years, the techniques standardly used in neurobiological research are somewhat rudimentary, such as looking at image slices or maximal intensity projections. Thus there is a real demand from neurobiologists, and biologists in general, for a flexible visualization tool that allows interactive visualization of multi-channel confocal data, with rapid fine-tuning of parameters to reveal the three-dimensional relationships of structures of interest. Together with neurobiologists, we have designed such a tool, choosing visualization methods to suit the characteristics of confocal data and a typical biologist's workflow. We use interactive volume rendering with intuitive settings for multidimensional transfer functions, multiple render modes and multi-views for multi-channel volume data, and embedding of polygon data into volume data for rendering and editing. As an example, we apply this tool to visualize confocal microscopy datasets of the developing zebrafish visual system.
Original languageEnglish (US)
Pages (from-to)1489-1496
Number of pages8
JournalIEEE Transactions on Visualization and Computer Graphics
Volume15
Issue number6
DOIs
StatePublished - Nov 2009
Externally publishedYes

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): KUS-C1-016-04
Acknowledgements: We wish to acknowledge the following funding: NIH R01-EY12873, Dana Foundation, NSF: CNS-0615194, CNS-0551724,CCF-0541113, IIS-0513212, DOE VACET SciDAC, KAUST GPRKUS-C1-016-04.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.

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