ZFIN ID: ZDB-PUB-171025-11
FluoRender: joint freehand segmentation and visualization for many-channel fluorescence data analysis
Wan, Y., Otsuna, H., Holman, H.A., Bagley, B., Ito, M., Lewis, A.K., Colasanto, M., Kardon, G., Ito, K., Hansen, C.
Date: 2017
Source: BMC Bioinformatics   18: 280 (Journal)
Registered Authors: Otsuna, Hideo
Keywords: Analysis, FluoRender, Freehand segmentation, GPUs, Multichannel, Visualization, Volume data
MeSH Terms:
  • Algorithms
  • Animals
  • Batrachoidiformes/metabolism
  • Extremities/anatomy & histology
  • Eye/anatomy & histology
  • Eye/pathology
  • Image Processing, Computer-Assisted
  • Imaging, Three-Dimensional
  • Mice
  • Microscopy, Fluorescence
  • Software*
  • Zebrafish/anatomy & histology
  • Zebrafish/physiology
PubMed: 28549411 Full text @ BMC Bioinformatics
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.
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.
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.