KAUST Grant NumberKUS-C1-016-04
Online Publication Date2013-07-01
Print Publication Date2013-06
Permanent link to this recordhttp://hdl.handle.net/10754/599607
MetadataShow full item record
AbstractBrainbow is a genetic engineering technique that randomly colorizes cells. Biological samples processed with this technique and imaged with confocal microscopy have distinctive colors for individual cells. Complex cellular structures can then be easily visualized. However, the complexity of the Brainbow technique limits its applications. In practice, most confocal microscopy scans use different florescence staining with typically at most three distinct cellular structures. These structures are often packed and obscure each other in rendered images making analysis difficult. In this paper, we leverage a process known as GPU framebuffer feedback loops to synthesize Brainbow-like images. In addition, we incorporate ID shuffing and Monte-Carlo sampling into our technique, so that it can be applied to single-channel confocal microscopy data. The synthesized Brainbow images are presented to domain experts with positive feedback. A user survey demonstrates that our synthetic Brainbow technique improves visualizations of volume data with complex structures for biologists.
CitationWan Y, Otsuna H, Hansen C (2013) Synthetic Brainbows. Computer Graphics Forum 32: 471–480. Available: http://dx.doi.org/10.1111/cgf.12134.
SponsorsThis research was sponsored by NIH-1R01GM098151-01, the DOE NNSA Award DE-NA0000740, KUS-C1-016-04 made by King Abdullah University of Science and Technology (KAUST), DOE SciDAC Institute of Scalable Data Management Analysis and Visualization DOE DE-SC0007446, NSF OCI-0906379, NSF IIS-1162013. We would like to thank A. Kelsey Lewis and her colleagues of the Department of Human Genetics at the University of Utah for a good explanation of the Brainbow technique. We also want to thank all the biologists participated in the survey. The reviewers' comments are very encouraging and helpful to us.
JournalComputer Graphics Forum
PubMed Central IDPMC4091929
CollectionsPublications Acknowledging KAUST Support
- Brainbow: new resources and emerging biological applications for multicolor genetic labeling and analysis.
- Authors: Weissman TA, Pan YA
- Issue date: 2015 Feb
- Visualizing the Developing Brain in Living Zebrafish using Brainbow and Time-lapse Confocal Imaging.
- Authors: Cook ZT, Brockway NL, Weissman TA
- Issue date: 2020 Mar 23
- An analytical tool that quantifies cellular morphology changes from three-dimensional fluorescence images.
- Authors: Haass-Koffler CL, Naeemuddin M, Bartlett SE
- Issue date: 2012 Aug 31
- Improved tools for the Brainbow toolbox.
- Authors: Cai D, Cohen KB, Luo T, Lichtman JW, Sanes JR
- Issue date: 2013 Jun
- Correlative scanning electron and confocal microscopy imaging of labeled cells coated by indium-tin-oxide.
- Authors: Rodighiero S, Torre B, Sogne E, Ruffilli R, Cagnoli C, Francolini M, Di Fabrizio E, Falqui A
- Issue date: 2015 Jun