FluoroSim: A Visual Problem-Solving Environment for Fluorescence Microscopy

Cory W. Quammen, Alvin C. Richardson, Julian Haase, Benjamin D. Harrison, Russell M. Taylor, Kerry S. Bloom
Department of Computer Science, UNC Chapel Hill, USA
Eurographics Workshop Vis Comput Biomed. 2008 January 1; 2008: 151-158


   title={FluoroSim: A Visual Problem-Solving Environment for Fluorescence Microscopy},

   author={Quammen, C.W. and Richardson, A.C. and Haase, J. and Harrison, B.D. and Taylor, R.M. and others},

   booktitle={Eurographics Workshop on Visual Computing for Biomedicine},




   organization={NIH Public Access}


Fluorescence microscopy provides a powerful method for localization of structures in biological specimens. However, aspects of the image formation process such as noise and blur from the microscope’s point-spread function combine to produce an unintuitive image transformation on the true structure of the fluorescing molecules in the specimen, hindering qualitative and quantitative analysis of even simple structures in unprocessed images. We introduce FluoroSim, an interactive fluorescence microscope simulator that can be used to train scientists who use fluorescence microscopy to understand the artifacts that arise from the image formation process, to determine the appropriateness of fluorescence microscopy as an imaging modality in an experiment, and to test and refine hypotheses of model specimens by comparing the output of the simulator to experimental data. FluoroSim renders synthetic fluorescence images from arbitrary geometric models represented as triangle meshes. We describe three rendering algorithms on graphics processing units for computing the convolution of the specimen model with a microscope’s point-spread function and report on their performance. We also discuss several cases where the microscope simulator has been used to solve real problems in biology.
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