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BioLaser: Establishing a High-Resolution Laser Ablation Tomography Platform for UK Bioimaging Research


Type

Thesis

Change log

Authors

Atkin, Peter 

Abstract

High-resolution 3D tomographic imaging of botanical materials can provide enormous insight into questions regarding relationships between structure and function. The National Institute for Agricultural Botany (NIAB) sponsored this body of work to meet an unfilled imaging niche for a tomographic device capable of imaging a wide range of heterogeneous, opaque plant materials in volumes of (0.1 mm)3 to (2 mm)3 with a resolution of ~0.1 μm – 10 µm. Other requirements included automated high-throughput processing, high design flexibility, and quantifiable sectioning measurement. Whilst some technologies do exist with the potential to fill this niche, they suffer from one or more of the following issues: too time consuming; too labour intensive; unreliable for hard woody materials; inflexible; too expensive; lacking the type of imaging contrast required to generate useful data. In response to these requirements a novel proof-of-concept ultrafast laser ablation tomography system named “BioLaser” was proposed. A proof-of-concept BioLaser system has been built using an existing ultrafast laser platform as a base. Several interchangeable high-resolution microscopes are integrated, as well as a chromatic confocal probe topographic measurement device to facilitate layer removal measurement and to assist in automation. Bespoke software has also been developed, providing automation and functionality of the proof-of-concept BioLaser system. Precision alignment, calibration, and error budgeting was conducted to ensure system’s accuracy is in line with the given BioLaser criteria. Ultrafast ablation characterisation of a chosen heterogenous plant material, mature wheat seed endosperm, has been conducted for the first time to examine the influence of ultrafast laser parameters on the ablation mechanisms of botanical samples. Functional ablation thresholds of this heterogenous material have also been established. Further to this, ultrafast ablation parameters have been optimised based on the key tomographic sectioning parameters of material removal rate, exposed surface flatness, and exposed surface damage. Optimisation was conducted with the aid of JMP® statistical software. An average material removal rate of 1.97 x 105 µm3/s has been achieved using a 1030 nm wavelength, 280 fs pulse length laser, optimised to achieve a maximum surface variation of ±10 µm whilst exhibiting no measurable indication of chemical or thermal degradation of the exposed surface. This approximately doubles the maximum ultrafast volume ablation rate given in literature. Applications studies have also been successfully conducted to demonstrate the functionality of the proof-of-concept BioLaser system and optimised ultrafast ablation parameters across a range of relevant and challenging botanical samples. Some of the applications of BioLaser demonstrated include the automatic exposure and measurement of A-type starch granules in wheat seed endosperm, the high-resolution tomographic imaging of dried oat stems, and the successful tracking of vessels through green brachypodium node. This thesis lays the foundation for a high-resolution ultrafast laser ablation tomography platform for botanical research.

Description

Date

2022-01-05

Advisors

O'Neill, William
Sparkes, Martin

Keywords

Ultrafast Lasers, Laser Ablation Tomography, Ultra-Precision, Machine Design, Botanical Samples, Multi-Variable Optimisation, Heterogenous Material Ablation Characterisation

Qualification

Doctor of Philosophy (PhD)

Awarding Institution

University of Cambridge
Sponsorship
EPSRC (1802556)
EPSRC (Engineering and Physical Sciences Research Council); NIAB (National Institute for Agricultural Botany)