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Interactive Multichannel Fluorescence Data Visualization and Analysis

Chi-Bin Chien
Brig Bagley

FluoRender is an interactive tool for neurobiologists to visualize confocal microscopy data in their research. Multiple channels, detailed three-dimensional structures, and time-dependent sequences are the three major features of confocal microscopy data. With these features and usability in mind, we designed and engineered our system, which is now a free package for public download. We present the visualization pipeline and main features of our system for 3D/4D multi-channel confocal data visualization. Our system supports different input formats commonly seen for confocal microscopy. By minimizing pre-processing and optimizing data reading codes, it can read 3D/4D data with minimal latency. It has easy-to-use parameters for volume rendering effects, which are adjusted with real-time speed. It uses several image post-processing methods for detail enhancement, which are applied after volumetric data are rendered, and thus their adjustments are real-time even for 4D sequences. For multi-channel data, our system supports three different blending modes and channel grouping. Users can easily change all the settings and emphasize the most important features.

Release Date:
December, 2016
Data type:
2D, 3D, Spatial representation, Temporal animation
Interactive 3D painting, 3D measurements, Graph-based dense tracking, Multichannel streaming
Installed, Algorithm
OpenGL, GLSL, OpenCL, C++
Mac OSX, Windows
Minimum OpenGL v3.3 support, Minimum OpenCL v1.2 support

Project development

Institution: SCI Institute and the School of Computing, Department of Neurobiology and Anatomy, University of Utah

This publication is based on work supported by Award No. KUS-CI-016-04, made by King Abdullah University of Science and Technology (KAUST), DOE SciDAC:VACET, NSF OCI-0906379, NIH-1R01GM098151-01.