Physically-based in silico light sheet microscopy for visualizing fluorescent brain models

BMC Bioinformatics
Marwan AbdellahFelix Schürmann

Abstract

We present a physically-based computational model of the light sheet fluorescence microscope (LSFM). Based on Monte Carlo ray tracing and geometric optics, our method simulates the operational aspects and image formation process of the LSFM. This simulated, in silico LSFM creates synthetic images of digital fluorescent specimens that can resemble those generated by a real LSFM, as opposed to established visualization methods producing visually-plausible images. We also propose an accurate fluorescence rendering model which takes into account the intrinsic characteristics of fluorescent dyes to simulate the light interaction with fluorescent biological specimen. We demonstrate first results of our visualization pipeline to a simplified brain tissue model reconstructed from the somatosensory cortex of a young rat. The modeling aspects of the LSFM units are qualitatively analysed, and the results of the fluorescence model were quantitatively validated against the fluorescence brightness equation and characteristic emission spectra of different fluorescent dyes. Modelling and simulation.

References

Jan 24, 2006·Nature Reviews. Neuroscience·Henry Markram
Feb 7, 2007·Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society·Antti LehmussolaOlli Yli-Harja
Jul 26, 2007·IEEE Transactions on Medical Imaging·Antti LehmussolaOlli Yli-Harja
Feb 2, 2008·IEEE Transactions on Systems, Man, and Cybernetics. Part B, Cybernetics : a Publication of the IEEE Systems, Man, and Cybernetics Society·F Kagalwala, T Kanade
May 5, 2009·Journal of the Optical Society of America. A, Optics, Image Science, and Vision·Heidy SierraDana H Brooks
May 20, 2009·BioTechniques·Peter A SantiJames R Leger
Feb 23, 2011·The Journal of Histochemistry and Cytochemistry : Official Journal of the Histochemistry Society·Peter A Santi
Mar 9, 2011·IEEE Transactions on Visualization and Computer Graphics·Sébastien LasserreHenry Markram
Mar 26, 2013·Nature Methods·Misha B AhrensPhilipp J Keller
Jun 20, 2014·Nature Protocols·Raju TomerKarl Deisseroth

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Citations

Mar 16, 2016·Biomedical Optics Express·A K GlaserJ T C Liu
Sep 4, 2015·BMC Bioinformatics·Jan AertsDaniel Weiskopf
Jan 9, 2019·Frontiers in Neuroinformatics·Espen HagenGaute T Einevoll
May 28, 2019·Frontiers in Neuroinformatics·Xue Fan, Henry Markram

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Methods Mentioned

BETA
fluorescence
imaging technique
Fluorescence Microscopy

Software Mentioned

PBRT based Rendering Toolkit
PBRT
LuxRender
Mitsuba

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