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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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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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 |
format | Online Article Text |
id | pubmed-4547197 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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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