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

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TitlePhysically-based in silico light sheet microscopy for visualizing fluorescent brain models
Publication TypeJournal Article
Year of Publication2015
AuthorsAbdellah, M, Bilgili, A, Eilemann, S, Markram, H, rmann, Fü
JournalBMC Bioinformatics
IssueSuppl 11
Date PublishedJan-01-2015
KeywordsFluorescence Rendering and Visualization, In Silico Neuroscience, Light Sheet Fluorescence Microscopy, Modelling and Simulation, Neocortical Brain Models


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.

Short TitleBMC BioinformaticsBMC Bioinformatics