Video-rate volumetric neuronal imaging using 3D targeted illumination

Fast volumetric microscopy is required to monitor large-scale neural ensembles with high spatio-temporal resolution. Widefield fluorescence microscopy can image large 2D fields of view at high resolution and speed while remaining simple and costeffective. A focal sweep add-on can further extend the capacity of widefield microscopy by enabling extended-depth-of-field (EDOF) imaging, but suffers from an inability to reject out-of-focus fluorescence background. Here, by using a digital micromirror device to target only in-focus sample features, we perform EDOF imaging with greatly enhanced contrast and signal-to-noise ratio, while reducing the light dosage delivered to the sample. Image quality is further improved by the application of a robust deconvolution algorithm. We demonstrate the advantages of our technique for in vivo calcium imaging in the mouse brain.This work was funded by the National Institutes of Health (R21EY026310) and the National Science Foundation (CBET-1508988). The authors wish to thank E. McCarthy and Prof. M.J. Baum for providing mouse brain slices used in this manuscript, and A. I. Mohammed for providing in vivo mouse brain samples in the early stages of this work. (R21EY026310 - National Institutes of Health; CBET-1508988 - National Science Foundation)Published versio

Speeded-Up Focus Control of Electrically Tunable Lens by Sparse Optimization

Electrically tunable lenses (ETL), also known as liquid lenses, can be focused at various distances by changing the electric signal applied on the lens. ETLs require no mechanical structures, and therefore, provide a more compact and inexpensive focus control than conventional computerized translation stages. They have been exploited in a wide range of imaging and display systems and enabled novel applications for the last several years. However, the optical fluid in the ETL is rippled after the actuation, which physically limits the response time and significantly hampers the applicability range. To alleviate this problem, we apply a sparse optimization framework that optimizes the temporal pattern of the electrical signal input to the ETL. In verification experiments, the proposed method accelerated the convergence of the focal length to the target patterns. In particular, it converged the optical power to the target at twice the speed of the simply determined input signal, and increased the quality of the captured image during multi-focal imaging

High-speed imaging with optical encoding and compressive sensing

Imaging instruments can be used to obtain a series of frames in domains such as frequency and time. Recent advancements in applications such as medical astronomical, scientic and the consumer application, demand overall improvements in these imaging systems. Many current imaging methods rely on the well-known Shannon-Nyquist theorem where sustaining this conventional model increases the system complexity, data rate, storage and processing power as well as the overall build costs of these units. Recent investigations based on the mathematical theory of compressed sensing (CS) have broken the traditional sampling mechanisms and introduces alternative methods of data sampling. This dissertation investigates the current advancements in the high-speed imaging schemes and proposes new methods and optical designs to improve the spatial and temporal resolution as well as the required transmission and storage capacity of the imaging systems. First, we investigate the current mathematical models of CS based algorithms in video acquisition systems and propose an improved adapted technique for data reconstruction. Then we investigate the state-of-the-art high-speed imaging methods and introduce optical encoding techniques that enable the current high-speed imaging systems to reach 10 times faster frame rates whilst preserving the spatial resolution of the existing systems. Second, we develop a novel high-speed imaging system that implements CS based optical imaging technique and experimentally demonstrate the operation of this novel imaging system. The proposed compressive coded rotating mirror (CCRM) camera benefits from noticeably improved physical dimensions, highly reduced build costs and the significantly simplified operation compared to the other high-speed cameras. Due to the built-in optical encoding and on-the-fly compression functionalities of CCRM camera, it becomes a viable option for the fields such as the medical and military based imaging applications where the security of the data remains one of the top priorities in the imaging instruments. Finally, we discuss the potential improvements on the CCRM camera and propose several advancement plans for the future of this system

Computational Multispectral Endoscopy

Minimal Access Surgery (MAS) is increasingly regarded as the de-facto approach in interventional medicine for conducting many procedures this is due to the reduced patient trauma and consequently reduced recovery times, complications and costs. However, there are many challenges in MAS that come as a result of viewing the surgical site through an endoscope and interacting with tissue remotely via tools, such as lack of haptic feedback; limited field of view; and variation in imaging hardware. As such, it is important best utilise the imaging data available to provide a clinician with rich data corresponding to the surgical site. Measuring tissue haemoglobin concentrations can give vital information, such as perfusion assessment after transplantation; visualisation of the health of blood supply to organ; and to detect ischaemia. In the area of transplant and bypass procedures measurements of the tissue tissue perfusion/total haemoglobin (THb) and oxygen saturation (SO2) are used as indicators of organ viability, these measurements are often acquired at multiple discrete points across the tissue using with a specialist probe. To acquire measurements across the whole surface of an organ one can use a specialist camera to perform multispectral imaging (MSI), which optically acquires sequential spectrally band limited images of the same scene. This data can be processed to provide maps of the THb and SO2 variation across the tissue surface which could be useful for intra operative evaluation. When capturing MSI data, a trade off often has to be made between spectral sensitivity and capture speed. The work in thesis first explores post processing blurry MSI data from long exposure imaging devices. It is of interest to be able to use these MSI data because the large number of spectral bands that can be captured, the long capture times, however, limit the potential real time uses for clinicians. Recognising the importance to clinicians of real-time data, the main body of this thesis develops methods around estimating oxy- and deoxy-haemoglobin concentrations in tissue using only monocular and stereo RGB imaging data

Smart knives: controlled cutting schemes to enable advanced endoscopic surgery

With the backdrop of the rapidly developing research in Natural Orifice Transluminal Endoscopic Surgery (NOTES), analysis of the literature supported the view that inventing new, controlled tissue dissection methods for flexible endoscopic surgery may be necessary. The literature also confirmed that white space exists for research into and the development of new cutting tools. The strategy of “deconstructing dissection” proposed in this thesis may provide dissection control benefits, which may help address the unique manoeuvring challenges for tissue dissection at flexible endoscopy. This assertion was supported by investigating six embodiments of the strategy which provided varying degrees of enhanced tissue dissection control. Seven additional concepts employing the strategy which were not prototyped also were offered as potential solutions that eventually might contribute evidence in defence of the strategy. One concept for selective ablation — dye-mediated laser ablation — was explored in-depth by theoretical analysis, experimentation and computation. The ablation process was found to behave relatively similar to unmediated laser ablation, but also to depend on cyclic carbonisation for sustained ablation once the dye had disappeared. An Arrhenius model of carbonisation based on the pyrolysis and combustion of wood cellulose was used in a tissue ablation model, which produced reasonable results. Qualitative results from four methods for dye application and speculation on three methods for dye removal complete the framework by which dye-mediated laser ablation might deliver on the promise offered by “deconstructing dissection”. Overall, this work provided the “deconstructing dissection” strategic framework for controlled cutting schemes and offered plausible evidence that the strategy could work by investigating embodiments of the scheme. In particular, dye-mediated laser ablation can provide selective ablation of tissue, and a theoretical model for the method of operation was offered. However, some practical hurdles need to be overcome before it can be useful in a clinical setting

Microscopy and Analysis

Microscopes represent tools of the utmost importance for a wide range of disciplines. Without them, it would have been impossible to stand where we stand today in terms of understanding the structure and functions of organelles and cells, tissue composition and metabolism, or the causes behind various pathologies and their progression. Our knowledge on basic and advanced materials is also intimately intertwined to the realm of microscopy, and progress in key fields of micro- and nanotechnologies critically depends on high-resolution imaging systems. This volume includes a series of chapters that address highly significant scientific subjects from diverse areas of microscopy and analysis. Authoritative voices in their fields present in this volume their work or review recent trends, concepts, and applications, in a manner that is accessible to a broad readership audience from both within and outside their specialist area