FluoRender: joint freehand segmentation and visualization for many-channel fluorescence data analysis

Autor: Charles Hansen, Brig Bagley, Yong Wan, A. Kelsey Lewis, Gabrielle Kardon, Mary P. Colasanto, Kei Ito, Masayoshi Ito, Holly A. Holman, Hideo Otsuna
Jazyk: angličtina
Rok vydání: 2017
Předmět:
0301 basic medicine
GPUs
Computer science
Graphics hardware
ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION
Eye
lcsh:Computer applications to medicine. Medical informatics
Biochemistry
Rendering (computer graphics)
Mice
03 medical and health sciences
Imaging
Three-Dimensional
0302 clinical medicine
Structural Biology
Computer graphics (images)
Image Processing
Computer-Assisted
Animals
Segmentation
Computer vision
Volume data
Molecular Biology
lcsh:QH301-705.5
Zebrafish
Visualization
Freehand segmentation
FluoRender
business.industry
Applied Mathematics
Extremities
Image segmentation
Batrachoidiformes
Computer Science Applications
030104 developmental biology
Microscopy
Fluorescence
Biological data visualization
lcsh:Biology (General)
Compositing
RGB color model
Multichannel
lcsh:R858-859.7
Artificial intelligence
business
Software
Algorithms
030217 neurology & neurosurgery
Analysis
Communication channel
Zdroj: BMC Bioinformatics, Vol 18, Iss 1, Pp 1-15 (2017)
BMC Bioinformatics
ISSN: 1471-2105
DOI: 10.1186/s12859-017-1694-9
Popis: Background Image segmentation and registration techniques have enabled biologists to place large amounts of volume data from fluorescence microscopy, morphed three-dimensionally, onto a common spatial frame. Existing tools built on volume visualization pipelines for single channel or red-green-blue (RGB) channels have become inadequate for the new challenges of fluorescence microscopy. For a three-dimensional atlas of the insect nervous system, hundreds of volume channels are rendered simultaneously, whereas fluorescence intensity values from each channel need to be preserved for versatile adjustment and analysis. Although several existing tools have incorporated support of multichannel data using various strategies, the lack of a flexible design has made true many-channel visualization and analysis unavailable. The most common practice for many-channel volume data presentation is still converting and rendering pseudosurfaces, which are inaccurate for both qualitative and quantitative evaluations. Results Here, we present an alternative design strategy that accommodates the visualization and analysis of about 100 volume channels, each of which can be interactively adjusted, selected, and segmented using freehand tools. Our multichannel visualization includes a multilevel streaming pipeline plus a triple-buffer compositing technique. Our method also preserves original fluorescence intensity values on graphics hardware, a crucial feature that allows graphics-processing-unit (GPU)-based processing for interactive data analysis, such as freehand segmentation. We have implemented the design strategies as a thorough restructuring of our original tool, FluoRender. Conclusion The redesign of FluoRender not only maintains the existing multichannel capabilities for a greatly extended number of volume channels, but also enables new analysis functions for many-channel data from emerging biomedical-imaging techniques. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1694-9) contains supplementary material, which is available to authorized users.
Databáze: OpenAIRE
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