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

Handle URI:
http://hdl.handle.net/10754/597534
Title:
An interactive visualization tool for multi-channel confocal microscopy data in neurobiology research
Authors:
Yong Wan,; Otsuna, H.; Chi-Bin Chien,; Hansen, C.
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.
Publisher:
Institute of Electrical and Electronics Engineers (IEEE)
Journal:
IEEE Transactions on Visualization and Computer Graphics
KAUST Grant Number:
KUS-C1-016-04
Issue Date:
Nov-2009
DOI:
10.1109/TVCG.2009.118
PubMed ID:
19834225
PubMed Central ID:
PMC2874972
Type:
Article
ISSN:
1077-2626
Sponsors:
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.
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorYong Wan,en
dc.contributor.authorOtsuna, H.en
dc.contributor.authorChi-Bin Chien,en
dc.contributor.authorHansen, C.en
dc.date.accessioned2016-02-25T12:41:36Zen
dc.date.available2016-02-25T12:41:36Zen
dc.date.issued2009-11en
dc.identifier.issn1077-2626en
dc.identifier.pmid19834225en
dc.identifier.doi10.1109/TVCG.2009.118en
dc.identifier.urihttp://hdl.handle.net/10754/597534en
dc.description.abstractConfocal 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.en
dc.description.sponsorshipWe 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.en
dc.publisherInstitute of Electrical and Electronics Engineers (IEEE)en
dc.subjectconfocal microscopyen
dc.subjectneurobiologyen
dc.subjectqualitative analysisen
dc.subjectVisualizationen
dc.subjectvolume renderingen
dc.subject.meshUser-Computer Interfaceen
dc.titleAn interactive visualization tool for multi-channel confocal microscopy data in neurobiology researchen
dc.typeArticleen
dc.identifier.journalIEEE Transactions on Visualization and Computer Graphicsen
dc.identifier.pmcidPMC2874972en
dc.contributor.institutionScientific and Imaging Institute, University of Utah, USA. wanyong@cs.utah.eduen
kaust.grant.numberKUS-C1-016-04en

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