Holistic Monte-Carlo optical modelling of biological imaging

Carles, G. and Harvey, A. R. (2019) Holistic Monte-Carlo optical modelling of biological imaging. Scientific Reports, 9, 15832. (doi: 10.1038/s41598-019-51850-1) (PMID:31676825) (PMCID:PMC6825179)

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Abstract

The invention and advancement of biological microscopy depends critically on an ability to accurately simulate imaging of complex biological structures embedded within complex scattering media. Unfortunately no technique exists for rigorous simulation of the complete imaging process, including the source, instrument, sample and detector. Monte-Carlo modelling is the gold standard for the modelling of light propagation in tissue, but is somewhat laborious to implement and does not incorporate the rejection of scattered light by the microscope. On the other hand microscopes may be rigorously and rapidly modelled using commercial ray-tracing software, but excluding the interaction with the biological sample. We report a hybrid Monte-Carlo optical ray-tracing technique for modelling of complete imaging systems of arbitrary complexity. We make the software available to enable user-friendly and rigorous virtual prototyping of biological microscopy of arbitrary complexity involving light scattering, fluorescence, polarised light propagation, diffraction and coherence. Examples are presented for the modelling and optimisation of representative imaging of neural cells using light-sheet and micro-endoscopic fluorescence microscopy and imaging of retinal vasculature using confocal and non-confocal scanning-laser ophthalmoscopes.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Carles Santacana, Dr Guillem and Harvey, Professor Andy
Authors: Carles, G., and Harvey, A. R.
College/School:College of Science and Engineering > School of Physics and Astronomy
Journal Name:Scientific Reports
Publisher:Nature Publishing Group
ISSN:2045-2322
ISSN (Online):2045-2322
Copyright Holders:Copyright © 2019 The Authors
First Published:First published in Scientific Reports 9:15832
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
190490Engineering and Physical Sciences Doctoral Training Grant 2012-16Mary Beth KneafseyEngineering and Physical Sciences Research Council (EPSRC)EP/K503058/1Research and Innovation Services
173569Seeing within extended volumes and 3D structures: 3D imaging and applicationsGuillem Carles SantacanaLeverhulme Trust (LEVERHUL)ECF-2016-757P&S - Physics & Astronomy