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

BACKGROUND: 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 synthet...

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Detalles Bibliográficos
Autores principales: Abdellah, Marwan, Bilgili, Ahmet, Eilemann, Stefan, Markram, Henry, Schürmann, Felix
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547197/
https://www.ncbi.nlm.nih.gov/pubmed/26329404
http://dx.doi.org/10.1186/1471-2105-16-S11-S8
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author Abdellah, Marwan
Bilgili, Ahmet
Eilemann, Stefan
Markram, Henry
Schürmann, Felix
author_facet Abdellah, Marwan
Bilgili, Ahmet
Eilemann, Stefan
Markram, Henry
Schürmann, Felix
author_sort Abdellah, Marwan
collection PubMed
description BACKGROUND: 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. RESULTS: 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. AMS SUBJECT CLASSIFICATION: Modelling and simulation
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spelling pubmed-45471972015-09-10 Physically-based in silico light sheet microscopy for visualizing fluorescent brain models Abdellah, Marwan Bilgili, Ahmet Eilemann, Stefan Markram, Henry Schürmann, Felix BMC Bioinformatics Research BACKGROUND: 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. RESULTS: 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. AMS SUBJECT CLASSIFICATION: Modelling and simulation BioMed Central 2015-08-13 /pmc/articles/PMC4547197/ /pubmed/26329404 http://dx.doi.org/10.1186/1471-2105-16-S11-S8 Text en Copyright © 2015 Abdellah et al. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Abdellah, Marwan
Bilgili, Ahmet
Eilemann, Stefan
Markram, Henry
Schürmann, Felix
Physically-based in silico light sheet microscopy for visualizing fluorescent brain models
title Physically-based in silico light sheet microscopy for visualizing fluorescent brain models
title_full Physically-based in silico light sheet microscopy for visualizing fluorescent brain models
title_fullStr Physically-based in silico light sheet microscopy for visualizing fluorescent brain models
title_full_unstemmed Physically-based in silico light sheet microscopy for visualizing fluorescent brain models
title_short Physically-based in silico light sheet microscopy for visualizing fluorescent brain models
title_sort physically-based in silico light sheet microscopy for visualizing fluorescent brain models
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547197/
https://www.ncbi.nlm.nih.gov/pubmed/26329404
http://dx.doi.org/10.1186/1471-2105-16-S11-S8
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