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The development of optical projection tomography instrumentation and its application to in vivo three dimensional imaging of zebrafish

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Title: The development of optical projection tomography instrumentation and its application to in vivo three dimensional imaging of zebrafish
Authors: Davis, Samuel Pascal Xia
Item Type: Thesis or dissertation
Abstract: OPT is a three dimensional (3D) imaging technique that can produce 3D reconstructions of transparent samples, requiring only a widefield imaging system and sample rotation. OPT can be readily applied to chemically cleared samples, or to live transparent organisms such as nematodes or zebrafish. For preclinical imaging, there is a trade-off between optical accessibility and biological relevance to humans. Adult Danio rerio (zebrafish) represent a promising compromise, with greater homology to humans than smaller animals, and superior optical accessibility than mice. However, their size and physiology present a number of imaging challenges including non-negligible absorption and optical scattering, and limited time for image data acquisition if the fish are to be recovered for longitudinal studies. A key goal of this PhD thesis research was to develop OPT to address these challenges and improve in vivo imaging capabilities for this model organism. This thesis builds on previous work at Imperial where angularly multiplexed OPT using compressed sensing was developed and applied to in vivo imaging of a cancer-burdened adult zebrafish, with a sufficiently short OPT data acquisition time to allow recovery of the fish after anaesthesia. The previous cross-sectional study of this work was extended to a longitudinal study of cancer progression that I undertook. The volume and quality of data acquired in the longitudinal study presented a number of data processing challenges, which I addressed with improved automation of the data processing pipeline and with the demonstration that convolutional neural networks (CNN) could replace the iterative compressed sensing algorithm previously used to suppress artifacts when reconstructing undersampled OPT data sets. To address the issue of high attenuation through the centre of an adult zebrafish, I developed conformal-high-dynamic-range (C-HDR) OPT and demonstrated that it could provide sufficient dynamic range for brightfield imaging of such optically thick samples, noting that transmitted light images can provide anatomical context for fluorescence image data. To reduce the impact of optical scattering in OPT, I developed a parallelised quasi-confocal version of OPT called slice-illuminated OPT (slice-OPT) to reject scattered photons and demonstrated this with live zebrafish. To enable 3D imaging with short wave infrared (SWIR) light, without the requirement of an expensive Ge or InGaAs camera, I implemented a single pixel camera and demonstrated single-pixel OPT (SP-OPT) for the first time.
Content Version: Open Access
Issue Date: Oct-2019
Date Awarded: May-2020
URI: http://hdl.handle.net/10044/1/80690
DOI: https://doi.org/10.25560/80690
Copyright Statement: Creative Commons Attribution NonCommercial NoDerivatives Licence
Supervisor: French, Paul
McGinty, James
Sponsor/Funder: Engineering & Physical Sciences Research Council
British Heart Foundation
Cancer Research UK
Medical Research Council
Wellcome Trust (London, England)
Department: Physics
Publisher: Imperial College London
Qualification Level: Doctoral
Qualification Name: Doctor of Philosophy (PhD)
Appears in Collections:Physics PhD theses