Search

This thesis investigates the role of biological shape in optical and acoustic measurement systems. Landmark-based geometric morphometrics (GMM) is a method of biological shape quantification based on the relationship between landmarks placed at anatomical location. GMM enables robust statistical analysis, comparisons between shapes, and visualisation of shape changes. This thesis explores the application of GMM with optical imaging for in vivo interpretation of amphioxus nerve cord shape, and acoustic measurements of Antarctic krill to improve biomass estimates. Optical imaging was performed using optical coherence tomography (OCT), an in vivo, label free imaging modality. A longitudinal study of amphioxus using OCT was conducted to capture the shape of the nerve cord during tail regeneration. Evidence for axial variation in the shape of the amphioxus nerve cord was found, however this work primarily develops a methodology and further studies are recommended to draw robust conclusions. GMM was used to construct a catalogue of realistic krill shapes for use in target strength models. Target strength is a measure of backscattering efficiency, which scales acoustic density to biomass. Typically, target strength is modelled with a generic krill shape, and distributions of length, orientation, and wetmass. This thesis demonstrates the presence of scattering mechanism influenced by shape and use of a shape catalogue to capture variability in target strength otherwise neglected. An error budget for biomass estimates of krill was developed to investigate the influence of shape and orientation. Orientation was found to have the largest contribution to the measurement error of biomass. In some cases, narrow orientation distributions resulted in biologically implausible biomass estimates due to nulls in the relationship between target strength and orientation angle. These nulls are responsive to changes in shape, suggesting the implementation of a shape catalogue could improve the accuracy of biomass estimates.

The cornea, a transparent avascular tissue, is essential for human vision by accounting for approximately two-thirds optical power of the eye. Also, it plays as a structural barrier and protects the eye from infections. Corneal injuries or diseases are a leading cause of visual loss and even blindness. It is reported that 45 million people are affected by corneal blindness. The transplantation of a donor cornea to change the injured one is the gold standard treatment. However, a shortage of donors and a high probability of immune rejection are the primary reasons for establishing alternative tissue-engineered corneal equivalent models. Collagen scaffold is the most common material to replicate the native corneal stroma. However, there is limited knowledge on the influence of cell behaviours interaction with collagen matrix on the biomechanics of corneal stromal models. This thesis developed tissue-engineered corneal stromal models by collagen-based hydrogels incorporated with human corneal stromal cells to mimic the injured or pathophysiological altered corneal extracellular matrix (ECM). The first study of this thesis aimed at characterising the mechanical property of neo-tissue in the wounded corneal stromal model during wound healing with vibrational optical coherence elastography (OCE). The cross-sectional elastic modulus map was reconstructed based on the local strain of the model induced by mono-frequency vibration. Results showed that an increase in the stiffness of neo-tissue during wound healing was non-invasively and continuously monitored and finally became the same as normal tissue on day 13. In the next study, the viscoelastic properties of corneal stromal models were continuously investigated with air-pulse OCE over 11 days. These stromal models were fabricated with various initial collagen scaffold concentrations. An air-pulse OCE system was developed to induce and track the surface acoustic wave (SAW) on the surface of corneal stromal models. The viscoelastic parameters of stromal models were estimated by fitting the SAW phase velocity dispersion into a SAW dispersion model. The stromal models with lower initial collagen concentrations had a faster increase in viscoelastic parameters and higher values by the end of the culture period. Finally, artificial niches in an in vitro polydimethylsiloxane (PDMS) substrate and limbal niches in ex vivo cadaveric tissue of donors aged from 4 to 96 years were visualised with spectral-domain optical coherence tomography (SD-OCT). Vibrational OCE was utilised to characterise the mechanical property of the artificial niche and limbal niche. The results showed that the dimensions and biomechanical parameters of the limbal niche were significantly correlated with age. In conclusion, this thesis shows that the developed OCE techniques are able to non-invasively characterise and provide local elastic modulus of the tissue-engineered corneal stroma and donor limbal tissues. The findings of this thesis enhance our understanding of cell-matrix interactions in the cornea with two different pathophysiological conditions and also biomechanics of the limbal niche.

Ovarian cancer is the most lethal gynaecological disease in the developed world. The term ovarian cancer describes a heterogeneous group of tumours that grow in the ovary but are not necessarily of ovarian origin. There are several histotypes of ovarian tumours which show distinct cellular origin, molecular aberrations and disease progression in patients; however, this heterogeneity is not reflected in the treatments currently available. Epithelial ovarian cancer (also termed ovarian carcinoma) accounts for 90% of all ovarian cancer diagnoses; it encompasses all cancers that arise from the epithelium and involve the ovary. Ovarian carcinomas commonly spread along peritoneal surfaces, particularly the omentum, and invade superficially into tissues. This body of work shows the development of novel techniques to characterise the invasive behaviour of epithelial ovarian tumours. Firstly, cell lines and ascites were used to characterise the behaviour of epithelial ovarian tumours and identify differences between serous and non-serous ovarian carcinomas. Recent genomic analysis has shown that many of the most commonly used ovarian cancer cell lines have been mischaracterised, leading to erroneous conclusions and a gap in the translation of laboratory research into novel treatments for patients. The behaviour of 5 serous and 5 non-serous ovarian cancer cell lines was characterised using 2D migration, cell cycle parameters and 3D invasion behaviour into different substrates. This work shows that ovarian cancer cell lines derived from non-serous carcinomas migrate and invade more aggressively than those derived from high-grade serous carcinomas. These differences may reflect differences in the behaviour of the primary tumour types from which the cell lines were derived. Next, an imaging tool that allows long-term time-lapse imaging to investigate tumour invasion was developed. Optical coherence tomography (OCT) is a non-damaging imaging technique used clinically to investigate ocular disease in vivo. In this body of work, time-lapse imaging of ovarian cancer cell lines over 5 days was developed on a commercial OCT system. The establishment of time-lapse OCT imaging made it possible to visualise how different invasive patterns developed over time. Application of the optimised time-lapse imaging protocol to the study of cell lines facilitated the investigation of different invasive behaviours in more detail, resolving differences in phenotypic behaviour over time. Finally, to better understand the in vivo behaviour of ovarian tumours, a patient-specific ex vivo model was developed to investigate individual patient tumour behaviour. Explant cultures using patient-derived tumour and matched normal omentum were developed to better mimic in vivo invasive behaviour and imaged using OCT. Tissue slices and mechanically dissociated tumour cells were cultured with patient omentum and compared with in vitro derived collagen/fibroblast matrices, demonstrating retention of tumour viability over a 14 day period. Together these data show the development of novel techniques to characterise the invasive behaviours of epithelial ovarian tumours. This work provides evidence that time-lapse OCT is a promising and novel tool for the characterisation of tumour invasion in vitro. Applying this to ovarian cancer patient-derived matched tumour and omentum ex vivo provides the opportunity to assess patient-specific invasive behaviour. The optimisation and development of techniques described here can provide future opportunities to develop preclinical models to further our understanding and clinical management of ovarian tumours.

Introduction. Macrophages play a key role in atherosclerotic plaque instability, they engender plaque rupture, leading to thrombosis and myocardial infarction. Their detection in coronary artery plaques would enable stratification of patients for better treatment of "vulnerable" phenotypes. Intra-coronary Optical Coherence Tomography (OCT) enables visualisation of vulnerable plaque morphology and has the potential to detect the signal variance created by increased numbers of macrophages. Aims. Our aim was to enhance the detection of macrophages using OCT in combination with intracellular contrast agents; and to demonstrate it in-vitro, ex-vivo and in-vivo. This was first endeavoured using clinically approved ultra-small superparamagnetic particles of iron oxide (USPIOs): an MRI contrast agent which is readily uptaken by macrophages in coronary plaques. The second approach was to design a novel OCT contrast agent based on different lanthanide ions with either a carbonate or fluoride structure. Methods. A "phantom" artery model was designed and 3D printed for standardised in-vitro imaging with intra-coronary OCT. Particle-laden macrophages were tested in this system to determine OCT contrast enhancement. Cell viability assays were performed to determine toxicity of novel lanthanide particles. Aortic plaques of Apo-lipoprotein E knockout mice, treated with USPIO or saline were OCT imaged and sectioned for histological analysis. Patients presenting with acute coronary artery disease were randomised to receive USPIO or saline treatment, followed by OCT imaging of the culprit plaque and non-culprit control. The local pixel Standard Deviation (SD) of OCT images were processed in Matlab as a metric of contrast enhancement. A local SD hotspot visualisation tool was developed in Matlab for use with the phantom, murine and human OCT images. Results. In all 7 phantoms, USPIO-laden macrophages significantly increased the mean SD compared to untreated macrophages (p<0.001). USPIO treated mouse plaques (n=3) showed significantly higher mean SD than control plaques (n=3) (p<0.05). USPIO treated patients (n=8) demonstrated a significantly increased mean SD compared to control patients (n=10) in culprit and non-culprit plaques (p<0.05). Within patients the mean SD was significantly higher for culprit compared to non-culprit plaques in both USPIO and control groups. The initial OCT screening of 10 novel lanthanide particles revealed the carbonate structures to be most efficacious for contrast enhancement compared to the fluoride ones. Phantoms made with particle-laden macrophages revealed the Gadolinium carbonate particle with Polyacrylic acid coating to have the highest mean SD increase compared to untreated macrophages. This particle also showed low levels of cell toxicity. Conclusions. USPIO administration was associated with a significant increase in OCT contrast in a novel in-vitro phantom model, an ex-vivo atherosclerotic mouse study and in a human clinical trial. USPIO enhances the detection of macrophages and may facilitate patient stratification. Additionally, novel OCT contrast agents have been made which show great potential for further enhancing macrophage detection in this same context.

Mechanical properties of biological soft tissues are closely related to their underlying pathological conditions. In clinical practice, they have been widely recognized as a significant indicator to assist disease diagnosis. There has been enormous technical advancement in imaging modalities such as the magnetic resonance elastography (MRE) and the ultrasound elastography to quantify the mechanical properties. Although the magnetic resonance imaging (MRI) and the ultrasound imaging can penetrate deep inside the human body, the millimetre-scale spatial resolution has limited their applications in the early detection of superficial diseases such as skin abnormalities. This research thesis takes advantage of the surface acoustic wave optical coherence elastography (SAW-OCE) to provide high-resolution microstructure images and quantitative mechanical property estimates of skin tissues for aiding skin disease diagnosis. In this research project, contact mechanical stimulations and non-contact ultrasound were utilised to induce the SAWs on the specimen surface. Phase-sensitive optical coherence tomography system (PhS-OCT) was employed to image the microstructure of the specimen and to track the transient wave propagation inside the specimen. In a transversely heterogeneous material, the 2D Young’s modulus map was reconstructed based on the SAW group velocity with an improved time-of-flight method, i.e., the multi-kernel-weighted-averaging (MKWA) method. In a vertically heterogeneous material, the elasticity of each layer was evaluated by analysing the SAW phase velocity dispersion using a novel mathematical model, i.e., the weighted average phase velocity (WAPV) inversion model. In a homogeneous viscoelastic material, the complex modulus of the medium was estimated by assessing the SAW phase velocity dispersion with the SAW dispersion model. During the experiments, all the abovementioned techniques were initially validated using tissue-mimicking material (TMM) phantoms and then demonstrated on in-vivo human skin tissues. The results have shown that the proposed SAW-OCE techniques are capable of imaging the microstructure of biological tissues and quantifying the mechanical properties of homogeneous and heterogeneous TMM phantoms, as well as in-vivo human skin tissues at different sites noninvasively. It has the great clinical potential of utilizing SAW-OCE as an assistant tool for human skin disease diagnosis in the early stage.

Biomedicine requires highly sensitive and efficient light sensors to analyse light-tissue or light-sample interactions. Single-photon avalanche diode (SPAD) sensors implemented with complementary metal-oxide-semiconductor (CMOS) technology have a growing range of applications in this field. Single-photon detection coupled with integrated timing circuits enables us to timestamp each detected photon with high temporal resolution (down to picoseconds). Arrays of SPAD based pixels and CMOS technology offer massively parallel time-resolved single-photon counting for spectrally and temporally resolved analysis of various light phenomena. This thesis examines how time-resolved CMOS SPAD based line sensors with per pixel timing circuits can be utilized to advance biophotonic applications. The study focuses on improving the existing techniques of fluorescence and Raman spectroscopy, and demonstrates for the first time CMOS SPAD based detection in optical coherence tomography (OCT). A novel detection scheme is proposed combining low-coherence interferometry and time-resolved photon counting. In this approach the interferometric information is revealed from spectral intensity measurements, which is supplemented by time-stamping of the photons building up the spectra. Two CMOS SPAD line sensors (Ra-I and its improved version, Ra-II) were characterized and the effect of their parameters on the selected techniques was analysed. The thesis demonstrates the deployment of the Ra-I line sensor in time-resolved fluorescence spectroscopy with indications of the applicability in time-resolved Raman spectroscopy. The work includes integration of the sensor with surrounding electrical and optical systems, and the implementation of firmware and software for controlling the optical setup. As a result, a versatile platform is demonstrated capable of micro- and millisecond sampling of spectral fluorescence lifetime changes in a single transient of fast chemical reactions. OCT operating in the spectral domain traditionally uses CMOS photodiode and charge-coupled device (CCD) based detectors. The applicability of CMOS SPAD sensors is investigated for the first time with focus on the main limitations and related challenges. Finally, a new detection method is proposed relying on both the wave and particle nature of light, recording time-resolved interferometric spectra from a Michelson interferometer. This method offers an alternative approach to analyse luminous effects and improves techniques based on the light’s time of flight. As an example, a proof of concept study is presented for the removal of unwanted reflections from along the sample and the optical path in an OCT setup.

Diagnosis and monitoring progression of neurodegenerative diseases relies on the assessment of clinical symptoms such as cognitive impairment in Alzheimer`s disease (AD) and disability in Multiple Sclerosis (MS). Detection of molecular and morphological hallmarks in the brain or spinal cord is invasive, insensitive and expensive. It has been hypothesized that changes in the retina may mirror changes in the brain. In contrast to brain imaging, imaging the eye is quick, non-invasive, inexpensive and might offering a unique “window to the brain” To test this hypothesis eye imaging studies were set up of cohorts with different type of neurodegenerative conditions such as typical and atypical Alzheimer’s disease (AD) or Multiple Sclerosis (MS). In this thesis I report on results using optical coherence tomography (OCT) as “gold standard” in neuro ophthalmology, alongside with new eye imaging and testing modalities such as ultra-widefield laser scanning ophthalmoscopy imaging (UWFI), adaptive optics (AO) and widefield perimetry combined with recently developed image analysis methods and algorithms. In this thesis I present evidences that there are detectable changes on different eye imaging modalities that correlate with disease type and stage and outline how future studies will benefit from these results, studies that are already under way.

Age-related macular degeneration (AMD) is the most common cause of irreversible visual impairment in the western world. Multimodal imaging has contributed a lot into disease detection, diagnosis and management. The availability of multimodal imaging is an unprecedented advantageous opportunity into relating structure with function in the presence of disease. The Northern Ireland Cohort of Longitudinal study of Aging (NICOLA) is a population based study which was designed to understand what factors are related with healthy aging. The sampling was designed to recruit individuals aged over 50 years old and consisted of two parts, a home-based interview and a health assessment which included an ophthalmic component which comprised of multimodal retinal imaging. Those attending the health assessment were the pool from which participants to the current study were drawn. The Northern Ireland Sensory Aging study (NISA) is a prospective, case-control add-on study, which invited back persons from the main NICOLA study in order to assess in detail those who had early and/or intermediate AMD. The NISA study, involved detailed functional and structural phenotyping of these participants with the use of state-of-the-art psychophysical tests and retinal imaging modalities. Chapter 1 of this thesis is an overview of the knowledge acquired so far through research regarding the pathogenesis, risk factors, classification and effect of visual function of both AMD and its recently reported phenotype, reticular pseudodrusen/subretinal drusenoid deposits (RPD/SDD). Chapter 2, is an overview of the methods used to carry out the functional tests and imaging in the NISA study, as well as the rationale for inclusion of those assessments. In the same chapter, the effect of the time chosen to dark-adapt an individual, on their performance on a novel piece of equipment, the scotopic MAcular Integrity Assessment (MAIA, CenterVue, Padova, Italy) microperimeter, as well as the repeatability of the device are tested. In chapter 3, the rationale and methods of developing an optical coherence tomography (OCT)-based classification system for the NISA study are described, thus adhering to the need for an OCT-based classification for AMD. The colour fundus photography (CFP) and OCT characteristics, as well as the prevalence of AMD phenotypes, of the NISA study population are described. Based on CFP detection a frequency of 31.8% and 15.9% for early and intermediate AMD respectively, were found. Furthermore, RPD were found in 1.7% of the study population, a frequency which is in agreement with previous studies. Based on OCT imaging, 39.9% of the study eyes showed typical drusen, with 34.7% of those being of homogeneous internal reflectivity. Subretinal drusneoid deposits were present in 39.8%. This percentage is similar to previous rates reported from studies which used the OCT modality. Of those with SDD, 19.1% were stage 1, 16.8% stage 2 and 3.9% stage 3 SDD. Analysis of agreement between a well-established CFP with the OCT-based classification system developed for the NISA study, showed only slight agreement between the two, whereas substantial agreement between the standard and wide-field OCT lenses was found. In chapter 4 an assessment of the potential impact of AMD-related lesions on retinal structure took place. With the use of OCT segmentation analysis, it was found that for both the CFP and OCT-based classification systems, the RPE, outer retina and photoreceptor thicknesses can be good indicators to distinguish AMD from control individuals. Additionally, factors that related with the structure of the layers of interest, in the eccentricities assessed, were age, gender, spherical equivalent and smoking. Finally, the results of this chapter agree with previously published work stating that the total retina is thicker in AMD individuals in the foveal area and that the RPE is thicker at all eccentricities assessed. The volume of the RPE is also a reliable metric to distinguish those with AMD from controls as it was found to increase from one AMD stage to another. In chapter 5, the impact of the AMD-related lesions on visual function and the sensitivity of each test within the NISA test battery, to detect results outside a reference range of control participants were assessed. It was found in this chapter that only some of the tests could serve as good visual function metrics and distinguish AMD individuals from their counterparts in normal macular health, including low luminance visual acuity, low luminance deficit, contrast sensitivity, mesopic microperimetry and rod-intercept time. These tests were found to be able to make this distinction in both the CFP and OCT-based analysis. Finally, these were the tests that showed increased sensitivity as the percentage of patients falling outside the reference range, increased while moving from one group to another. In chapter 6, the OCT groups created initially, were reclassified based on the previous results into a graded severity scale. In this chapter it was found that the structure of the RPE and photoreceptors is significantly affected and that this significance, is increased while moving from one group to another. The RPE and photoreceptor thicknesses, can also still distinguish AMD from control individuals. In terms of the effect on visual function, the results of this chapter, suggest that visual performance declined while moving from one OCT group to another. This was more profound for low luminance visual acuity, low luminance deficit, contrast sensitivity, mesopic microperimetry and rod-intercept time. Finally, these tests are those that can reliably distinguish AMD individuals from controls. Chapter 7 concludes this thesis with a general discussion of the overall findings and makes suggestions for future directions of the research in general and how specific findings of the NISA study could be further extended.

People with Down’s syndrome (DS) are known to experience premature ageing and have a high propensity for clinical diagnosis of dementia due to Alzheimer’s disease (AD). In DS there is a unique and natural model of over-expression of amyloid-beta (Aβ) protein, the accumulation of which is proposed to be the central early event in the pathogenesis of AD. In DS, AD neuropathology is universally seen in the brain from the fourth decade. Identifying biomarkers are essential to the evaluation of future treatment trials. The retina has been shown to experience changes in patients with AD, such as retinal thinning, compared to age-matched controls. As an extension of the brain, the retina can be quickly and non-invasively imaged and may provide a proxy measure of brain changes in AD. Using optical coherence tomography (OCT), cross-sectional retinal examinations were completed in 50 people with DS aged 18 years and over. Comparisons between retinal thickness of the DS and control groups were examined, as well as the effect of age on thickness in both groups. For the DS group, further investigations were made into the relationships between retinal thickness and (i) cognitive performance, (ii) diagnosis of dementia, (iii) cortical thickness and, (iv) presence of Aβ binding in the brain. Contrary to expectations, people with DS had thicker retina compared to age-matched controls. In addition, normal age-related retinal thinning was not seen in the DS group. People with DS have a life-long overproduction of Aβ, deposits of which have been previously imaged in the retina. Aβ may be responsible both directly, through physical mass, and indirectly through inflammation as a response to Aβ, for increased retinal thickness in people with DS. Consequently, retinal thickness in DS may be a proxy measure of Aβ deposition in the retina. As part of a collaborative study, brain Aβ binding was measured using positron emission tomography neuroimaging in a subset of the DS group. Individuals with positive Pittsburgh compound [11C]-PIB (PIB) binding to Aβ displayed a trend towards having thinner retina than those with negative PIB binding. These results indicate that a shift towards thinning retina in people DS may reflect changes in brain pathology. Future studies are discussed which aim to investigate Aβ and Aβ driven pathology in the retina.

Optical Coherence Tomography (OCT) is an imaging technique that uses near infra-red light to non-invasively form cross-sectional images of specimens, in a similar way to ultrasound and RADAR. A number of research groups have used OCT to study natural and artificial carious lesions and to some extent erosive lesions. For this, a variety of in vitro models have been used. However, the exact mechanism by which these demineralised enamel lesions affect the OCT measurements is not fully understood. This remains a barrier to its adoption as both an analytical laboratory tool and a widespread technique in clinical dentistry. Therefore, the aim of this thesis was to develop an understanding of how different demineralised enamel lesions manifest in OCT measurements. This is necessary for the technique to become useful as an in vivo clinical measurement and imaging system. Consequently, this study was carried out in a controlled laboratory environment for which a novel specimen holder was designed. This mitigated against specimen movement and maintained specimen hydration, which can be a source of uncertainty in the measurements. A custom-built OCT microscope was used for this work, which enabled automation of experiments and continuous time-lapse OCT imaging over time periods of hours to several days. This enabled bovine enamel demineralisation dynamics to be captured during in vitro caries and erosion formation. The stability of the system also enabled direct comparison between the OCT measurements of the optical properties of different demineralisation models. To achieve these measurements, the OCT system was carefully characterised and compared to established profilometry measurements. Interestingly, this revealed that the experimental protocol used to obtain lesions for profilometry was not to be representative of the lesions formed and measured by OCT. This is an important point when interpreting OCT data in light of other techniques. A novel method of analysis was developed that uses longitudinal OCT image correlation to quantify early stage surface softening during erosion. By using OCT volumetric data, this technique was able to measure sub-resolution changes at the specimen surface. Early results also indicate sensitivity to remineralisation. This thesis shows that OCT is sensitive to different demineralisation models produced and measured under controlled conditions. New method of handling the data can observe changes not previously seen in OCT. However, further work is still required to understand the underlying physical changes that lead to this sensitivity in OCT.

Basic science and early clinical trial evidence suggest the safe diuretic drug amiloride, may exert a neuroprotective effect in multiple sclerosis (MS) through blockade of the acid sensing ion channel. Neuroprotective treatments are a key unmet need in multiple sclerosis. Optic neuritis (ON) is a discrete CNS inflammatory event leading to neuro-axonal injury in the optic nerve and retina. The optic nerve is part of the visual system, one of the most functionally and structurally eloquent systems in the central nervous system, which affords a number of unique modalities to assess neurodegeneration and neuroprotection. The visual system can be classified into two parts, the anterior and posterior visual systems, which are defined by the lateral geniculate nucleus, where the two components synapse. The extent of neurodegeneration following ON in the anterior visual system can be imaged in vivo through scanning laser polarimetry (GDx) and optical coherence tomography (OCT). The posterior visual system can be imaged by quantitative and functional magnetic resonance imaging (MRI) of the brain, giving insights into white matter structural integrity and cortical plasticity over time. Combining these modalities in a longitudinal study, allows assessment of the impact of neurodegeneration in the anterior visual system on neurodegeneration downstream in the posterior visual system and on changes in functional connectivity over time in the visual cortex. Furthermore, in the clinical trial setting the neuroprotective effect of any intervention both on direct anterior neurodegeneration and downstream processes can be assessed. The functional relevance of changes in all of these biomarkers can be tested through a number of visual measures, including low contrast visual acuity. In MS, the contribution of transsynaptic neurodegeneration to the global neuronal loss experienced by patients is an area of incomplete understanding. In addition, the role of the visual cortex, through neuroplasticity, in aiding visual recovery from optic neuritis, is unclear. To address these issues, this thesis reports the results of the first clinical trial of amiloride in ON, and shows that despite the pre- and early clinical evidence of neuroprotection of amiloride, no neuroprotective benefit was found. It goes on to explore reasons for this lack of effect including the finding of early retinal neurodegeneration in ON, and the need for early recruitment windows in the future. From there, it makes a detailed assessment of the longitudinal changes in retinal OCT for 12 months following ON, including a novel finding of the temporal evolution of inner nuclear layer swelling, previously reported only cross-sectionally. Next, for the first time macular retinal neurodegeneration is shown to influence diffusion tensor MRI derived measures of white matter integrity in the optic radiations, indicating transsynaptic neurodegeneration. Finally, longitudinal changes in resting state functional connectivity following ON are found in the visual system for the first time. The interaction between this cortical functional, retinal neurodegeneration and visual recovery is probed.

Cardiovascular disease is one of the leading causes of the mortality in the western world. Many imaging modalities have been used to diagnose cardiovascular diseases. However, each has different forms of noise and artifacts that make the medical image analysis field important and challenging. This thesis is concerned with developing fully automatic segmentation methods for cross-sectional coronary arterial imaging in particular, intra-vascular ultrasound and optical coherence tomography, by incorporating prior and tracking information without any user intervention, to effectively overcome various image artifacts and occlusions. Combinatorial optimisation methods are proposed to solve the segmentation problem in polynomial time. A node-weighted directed graph is constructed so that the vessel border delineation is considered as computing a minimum closed set. A set of complementary edge and texture features is extracted. Single and double interface segmentation methods are introduced. Novel optimisation of the boundary energy function is proposed based on a supervised classification method. Shape prior model is incorporated into the segmentation framework based on global and local information through the energy function design and graph construction. A combination of cross-sectional segmentation and longitudinal tracking is proposed using the Kalman filter and the hidden Markov model. The border is parameterised using the radial basis functions. The Kalman filter is used to adapt the inter-frame constraints between every two consecutive frames to obtain coherent temporal segmentation. An HMM-based border tracking method is also proposed in which the emission probability is derived from both the classification-based cost function and the shape prior model. The optimal sequence of the hidden states is computed using the Viterbi algorithm. Both qualitative and quantitative results on thousands of images show superior performance of the proposed methods compared to a number of state-of-the-art segmentation methods.

This work presents an effective methodology for measuring the depth-resolved 3D full-field deformation of semitransparent, light scattering soft tissues such as vertebrate eye cornea. This was obtained by performing digital volume correlation on optical coherence tomography volume reconstructions of silicone rubber phantoms and porcine cornea samples. Both the strip tensile tests and the posterior inflation tests have been studied. Prior to these tests, noise effect and strain induced speckle decorrelation were first studied using experimental and simulation methods. The interpolation bias in the strain results has also been analyzed. Two effective approaches have been introduced to reduce the interpolation bias. To extract material constitutive parameters from the 3D full-field deformation measurements, the virtual fields method has been extended into 3D. Both manually defined virtual fields and the optimized piecewise virtual fields have been developed and compared with each other. Efforts have also been made in developing a method to correct the refraction induced distortions in the optical coherence tomography reconstructions. Tilt tests of different silicone rubber phantoms have been implemented to evaluate the performance of the refraction correction method in correcting the distorted reconstructions.

Raman spectroscopy is a powerful tool in the field of biomedicine for disease diagnosis owing to its potential to provide the molecular fingerprint of biological samples. However due to the inherent weak nature of the Raman process, there is a constant quest for enhancing the sensitivity of this technique for enhanced diagnostic efficiency. This thesis focuses on achieving this goal by integrating advanced methods with Raman spectroscopy. Firstly this thesis explores the applicability of a laser based fluorescence suppression technique – Wavelength Modulated Raman Spectroscopy (WMRS) - for suppressing the broad luminescence background which often obscure the Raman peaks. The WMRS technique was optimized for its applications in single cell studies and tissue studies for enhanced sensing without compromising the throughput. It has been demonstrated that the optimized parameter would help to chemically profile single cell within 6 s. A two fold enhancement in SNR of Raman bands was demonstrated when WMRS was implemented in fiber Raman based systems for tissue analysis. The suitability of WMRS on highly sensitive single molecule detection techniques such as Surface Enhanced Raman Spectroscopy (SERS) and Surface Enhanced Resonance Raman Spectroscopy (SERRS) was also explored. Further this optimized technique was successfully used to address an important biological problem in the field of immunology. This involved label-free identification of major immune cell subsets from human blood. Later part of this thesis explores a multimodal approach where Raman spectroscopy was combined with Optical Coherence Tomography (OCT) for enhanced diagnostic sensitivity (>10%). This approach was used to successfully discriminate between ex-vivo adenocarcinoma tissues and normal colon tissues. Finally this thesis explores the design and implementation of a specialized fiber Raman probe that is compatible with surgical environments. This probe was originally developed to be compatible with Magnetic Resonance Imaging (MRI) environment. It has the potential to be used for performing minimally invasive optical biopsy during interventional MRI procedures.

The emergence of microneedle (MN) technologies offers a route for a pain free, straightforward and efficient way of transdermal drug delivery, but technological barriers still exist which pose significant challenges for manufacture of MN systems with high volume outputs at low cost. The main aim of this research was to develop new ways for MN manufacture primarily using micro-injection moulding processes with high performance engineering thermoplastics. During the moulding process these polymeric melts will be subjected to extreme stress and temperature gradients and detailed material characterisation combined with in-line monitoring is desirable to optimise the moulding parameters and will help in achieving sharp microneedles with acceptable quality. Hence high shear rheology of these selected materials was performed at wall shear rates carried out in excess of 107 s-1 over a range of temperatures to predict the flow behaviour of polymer melts at such high shear strain rates. This information was fed into injection moulding simulation software tools (Moldflow) to assist the MN production process design. The optimal design was then used to produce a full 3D solid model of the injection mould and mould insert. Furthermore various design of experiments were conducted considering input parameters such as injection pressure, injection speed, melt temperature, filling time and mould cavity temperature. Response variables including product quality and data acquired from the cavity pressure and temperature transducers were used to optimise the manufacturing process. The moulded MNs were geometrically assessed using a range of characterisation techniques such as atomic force microscopy, confocal microscopy and scanning electron microscopy. An attempt to make hollow MNs was performed and encountered many challenges like partial cavity filling and part ejection during processing. Studies were carried out to understand the problem and identified the major problem was in tool design and improvements to the moulding tool design were recommended. Plasma treatment and mechanical abrasion were employed to increase the surface energy of the moulded polymer surfaces with the aim of enhancing protein adsorption. Sample surface structures before and after treatment were studied using AFM and surface energies have been obtained using contact angle measurement and calculated using Owens-Wendt theory. Adsorption performance of bovine serum albumin and release kinetics for each sample set was assessed using a Franz diffusion cell. Results indicate that plasma treatment significantly increases the surface energy and roughness resulting in better adsorption and release of BSA. To assist design-optimisation and to assess performance, a greater understanding of MN penetration behaviour is required. Contact stiffness, failure strength and creep behaviour were measured during compression tests of MN against a steel surface, and in-vitro penetration of MNs into porcine skin. The MN penetration process into porcine skin was imaged using optical coherence tomography. Finally, a finite element model of skin was established to understand the effect of tip geometry on penetration. The output of findings from this research will provide proof of concept level development and understanding of mechanisms of MN penetration and failure, facilitating design improvements for micro-injection moulded polymeric MNs.

This thesis forms part of an ongoing long-term project to investigate the suitability of Doppler optical coherence tomography (OCT) as a measurement tool to investigate skin thickness and blood flow in patients with systemic sclerosis. There is a discussion of the characterisation of an electro-optic phase modulator for use in a Doppler OCT imaging system which is being built for the purpose of clinical studies. In addition to this the development of software for the same system is described. The work includes a comparison of two methods of obtaining Doppler information that were tested with the system; a phase resolved method and a correlation mapping method. Initial structural and Doppler images obtained using the system are presented. In addition to this the development of semi-automated software to measure skin thickness from both OCT and high frequency ultrasound images is discussed. The results of a study, for which this software was developed, into skin thickness measurements using both techniques in both patients with systemic sclerosis and healthy controls are presented. Both OCT and high frequency ultrasound were able to measure a statistically significant difference in epidermal thickness at multiple locations on the body. Finally, the modification of a freely available Monte Carlo simulation for light propagation in multi-layered tissue (MCML) to enable the simulation of structural and Doppler OCT images is covered. The simulation was able to extract the magnitude of the simulated flow accurately to within an order of magnitude, and after a simple filter was applied to eliminate fluctuations in the data the structure of the Doppler image closely matched what was modelled.

Needle-based interventions (NBIs) are procedures that require a minimally invasive approach to gain access to tissue structures of interest. Each year, more than 30 million of these interventions are performed in the US. Due to the lack of proper visual feedback guiding navigation, up to 33% of NBIs are associated with complications, incurring significant human and economic costs. The objective of my dissertation is to establish a new research paradigm shift in the methodology of NBIs through integrating a unique forward-imaging multi-contrast optical coherent tomography (MC-OCT) needle technology with advanced machine-learning- based computer-aided diagnosis algorithms. Optical coherence tomography (OCT) is a novel biomedical imaging technique which provides micron-level spatial resolution. Compared to conventional imaging modalities, it provides the imaging results with a lot more details of localized tissue. OCT has been widely used in various applications including ophthalmology, biopsy procedures, different disease diagnosis, etc. Furthermore, OCT can perform real-time imaging based on the high-speed scanner and data acquisitor. Therefore, OCT has the potential in real-time guidance in different NBIs. To successfully acquire depth-resolved imaging during surgeries, we developed forward-view endoscopic OCT systems using gradient-index (GRIN) lenses. Additionally, we utilized polarization-sensitive OCT (PS-OCT) and Doppler OCT to build MC-OCT for enhanced tissue contrast and at-risk blood vessels detection. PS-OCT is a function extension of traditional OCT because it provides polarization-related biological features based on birefringence and diattenuation phenomena. Doppler OCT is effective in fluid flow imaging, so we utilized it for blood flow detection. By introducing PS-OCT and Doppler OCT, our endoscopic MC-OCT systems have been proved to be feasible in recognizing different tissue type and blood vessels. In this dissertation, we demonstrated endoscopic MC-OCT systems in surgical navigations in different NBIs including percutaneous nephrostomy (PCN), epidural anesthesia, Veress needle for pneumoperitoneum establishment, and different cancer diagnosis. To improve the working efficiency and reduce learning curves, we further applied deep learning methods in our studies to automate the navigation procedures. Different architectures were tested for tissue classifications and blood vessel detections. This innovated imaging platform has established a paradigm shift, offering the potential for widespread applications across various NBIs.

Sensory adaptation to blur improves visual acuity under defocused conditions. This phenomenon has been successfully demonstrated using subjective measures of acuity and is known as blur adaptation. This study investigates aspects of the mechanism of blur adaptation in human vision using subjective and objective methods. Parafoveal visual acuity measured under defocused conditions demonstrates that blur adaptation is not limited to the fovea. The presence of the adaptive mechanism in the parafovea also suggests that the neural compensation that takes places under defocused conditions acts across a spatial range and is not limited to specific frequency bands. An evaluation of the contrast sensitivity function under defocus provides further evidence. Electrophysiological methods measure the effect of blur adaptation at the retina and at the visual cortex to provide objective evidence for the presence of the blur adaptation mechanism. Finally enhanced-depth imaging optical coherence tomography examines whether a period of prolonged defocus triggers any short-term changes in choroidal thickness in a similar manner to that reported in animal emmetropisation.

Dental erosion has been defined as a chemical process that involves the dissolution of enamel and dentine by acid(s) not derived from bacteria when the surrounding aqueous phase is under-saturated with tooth mineral. Clinically however, dental erosion hardly ever occurs exclusively from the other modes of tooth wear such as abrasion and attrition. Hence the term erosive wear has been proposed and used to describe erosion-facilitated wear.With the prevalence of erosive wear being reported to be on the rise among children and adolescents in many countries, a plethora of oral health products such as dentifrices and mouth rinses had been put forward with claims of increasing the resistance of the enamel and / or dentine from being demineralised. However, the efficacy of these oral health products is still widely questionable as the studies carried out were mainly in vitro and / or in situ studies and the contradictory results were reported by different groups of researchers.The above mentioned discrepancies are often due to non-standardised in vitro and in situ study designs of erosion studies. Parameters such as type of acid used, concentration of acid used, duration of acid exposure, inclusion or exclusion of abrasion in the study model, ex vivo or in vivo acid challenge, ex vivo or in vivo treatment with oral health product and the nature of pellicle on the specimen are often varied.The availability of an detection tool which could be used to measure demineralisation on natural tooth surface in vivo would exclude many of the inevitable variability in in situ and in vitro study design, such as the simulation of the intra oral conditions in which the erosion challenge and intervention take place and the nature of the pellicle formed on the specimens. Hence with an in vivo detection tool, it is hopeful that the efficacy of any interventions would be evaluated more accurately and its results expounded to a wider context. It would be useful if the tool was sensitive to the very early stages of the erosion process as this would entail shorter and more economical study designs. Arising from the problems discussed above, potential non-invasive assessment methods that could be used clinically to measure demineralisation were explored and it was found that two optical methods, Optical Coherence Tomography (OCT) and Quantitative Light-induced Fluorescence (QLF) were potential methods for the tasks.The studies described in this thesis were divided into three main big sections; the first being the in vitro validation work of the two optical methods (Chapter 5 and 6), the second, validation of these methods in situ (Chapter 7) and finally the assessment of the efficacy of a high fluoride dentifrice on early enamel erosion using these two methods (Chapter 8).In the in vitro validation (Chapter 5), it was demonstrated that both QLF and OCT were able to detect erosion-interval related changes in natural surface samples eroded with orange juice for 60 minutes. However, results of Multiple Linear Regression and Paired t test suggest that QLF was more sensitive than OCT in the detection of demineralisation changes in this particular experimental setting. QLF demonstrated a R2 value of 0.590 while the best of the OCT outcome measure demonstrated a R2 value of 0.319.Further in vitro study (Chapter 6) was performed to explore the use of a moistened-exposed surface as a reference method for both OCT and QLF as it was felt that it would be beneficial if a coated reference area which posts as an additional step for error could be done away with. Results of this study showed that the moistened-exposed surface could be used a reference method for QLF only but not for OCT. Furnished with the findings of the above mentioned in vitro validation studies, an in situ validation of both the optical methods was performed (Chapter 7). It was found that OCT and QLF were able to longitudinally measure in situ demineralisation on polished and natural surfaced enamel which were subjected to 150 minutes of in vivo exposure to orange juice. Similar to the results of the in vitro study, QLF was found to be more sensitive than OCT in the detection of demineralisation changes on natural surfaced enamel. The last in situ study (Chapter 8) was to evaluate whether there was a protective effect of treating human enamel with a high-concentrated fluoride dentifrice during an active erosion phase and whether OCT and QLF were able to detect the protective effect. It was found that treating natural surface enamel with a 5000ppm NaF dentifrice increased its resistance against concurrent in vivo erosive challenge with an orange juice challenge. QLF was able to detect the protective effect of the 5000ppm NaF dentifrice on natural surface enamel against early in vivo erosion with an orange juice challenge regime while OCT did not.

In the medical field, the detection and diagnosis of diseases continue to improve. Developments in diagnostic techniques have helped to improve treatment in the early stages and avoid many risks to patients. One relatively new diagnostic technique is optical coherence tomography (OCT), which is used in many medical applications to perform internal microstructure imaging of the human body at high resolution (typically 10 micro metre), at high speed and in real time. OCT is non-invasive and can be used as a contact or non-contact technique to obtain an image. In medicine, there are many applications that involve OCT, such as in ophthalmology, gastroenterology, cardiology and oncology. This work demonstrates the design, development and implementation of a high resolution swept laser OCT system for the imaging and diagnosis of tissues in laboratory and clinical experiments. It reports an investigation to measure the thickness of the peritoneal membrane and the use of optical imaging contrast agents such as gold nanorods. There is also an account of the design of an endoscope-catheter fast scanning OCT system for biomedical studies of the gastrointestinal tract and gynaecological areas. These results were achieved by using a swept tuneable laser source with a very high tuning speed of 16 kHz over a wide range of wavelengths: 1260 nm to 1390 nm. The laser sweeps across 110 nm at a 16 kHz repetition rate. The real axial line speed is limited by the source that is used in the OCT system. The axial resolution of the system is 7 µm and its transverse resolution is 15 µm. The bandwidth of the source is up to DeltaGamma = 110 nm, centred at Gamma0 = 1325 nm, and the coherent length is 7 µm. On the sample arm of the interferometer, the swept laser OCT technique is combined with an optical probe and endoscope in order to develop a novel diagnostic imaging device to visualize tissue in vivo for animal and human experimental trials.

A new approach to the absolute measurement of two-dimensional optical path differences is presented in this thesis. The method, which incorporates a white light interferometer and a hyperspectral imaging system, is referred to as Hyperspectral Interferometry. A prototype of the Hyperspectral Interferometry (HSI) system has been designed, constructed and tested for two types of measurement: for surface profilometry and for depth-resolved displacement measurement, both of which have been implemented so as to achieve single shot data acquisition. The prototype has been shown to be capable of performing a single-shot 3-D shape measurement of an optically-flat step-height sample, with less than 5% difference from the result obtained by a standard optical (microscope) based method. The HSI prototype has been demonstrated to be able to perform single-shot measurement with an unambiguous 352 (m depth range and a rms measurement error of around 80 nm. The prototype has also been tested to perform measurements on optically rough surfaces. The rms error of these measurements was found to increase to around 4× that of the smooth surface. For the depth-resolved displacement field measurements, an experimental setup was designed and constructed in which a weakly-scattering sample underwent simple compression with a PZT actuator. Depth-resolved displacement fields were reconstructed from pairs of hyperspectral interferograms. However, the experimental results did not show the expected result of linear phase variation with depth. Analysis of several possible causes has been carried out with the most plausible reasons being excessive scattering particle density inside the sample and the possibility of insignificant deformation of the sample due to insufficient physical contact between the transducer and the sample.

Amblyopia is the leading cause of monocular visual impairment in children. Therapy for amblyopia is extremely beneficial in some children but ineffective in others. It is critical that the reasons for this discrepancy are understood. Emerging evidence indicates that current clinical protocols for the diagnosis of amblyopia may not be sufficiently sensitive in identifying individuals who, on more detailed examination, exhibit subtle structural defects of the eye. Presently, the magnitude of this problem is unknown. The aim of this study was to establish the prevalence of subtle retinal/optic nerve head defects in eyes diagnosed with amblyopia, to distinguish between possible explanations for the origin of such defects and to investigate the relationship between quantitative measures of retinal structure, retinal nerve fibre layer thickness and optic nerve head dimensions. Using the imaging technique of Optical Coherence Tomography (OCT) retinal structure has been investigated in detail, following the visual pathway across the retina from the fovea, via the paramacular bundle to the optic disc, where peripapillary retinal nerve fibre thickness has been imaged and subjected to detailed measures along with optic disc size and shape. The study formed two phases, the first imaging the eyes of visually normal adults and children, comparing them to amblyopes, both adults and children who had completed their treatment. The second phase, a longitudinal study, investigated retinal structure of amblyopic children undertaking occlusion therapy for the first time. By relating pre-therapy quantitative measures to the visual outcome the second phase of the study aimed to examine whether OCT imaging could identify children achieving a poor final outcome. The results show a clear picture of inter-ocular symmetry structure in all individuals, visually normal and amblyopic. Optic disc characteristics revealed no structural abnormalities in amblyopes, in any of the measured parameters, nor was there any association between the level of visual acuity and the measured structure. At the fovea differences were shown to occur in the presence of amblyopia, with thickening of the fovea and reduction of the foveal pit depth. The structural changes were found to be both bilateral and symmetrical with the fellow eye also affected. In the longitudinal phase of the study these changes were demonstrated to a greater extent in children who 'failed' to respond to treatment. This bilateral, symmetrical structural change found at the fovea, which has not been previously reported, cannot therefore be the primary cause of the visual loss which has been diagnosed as amblyopia.

The utilisation of near-infrared Raman spectroscopy for the discrimination of cancers and pre-cancers from normal tissue in the acro-digestive tract has been evaluated. A commercially available Raman microspectrometer has been modified to provide optimum throughput, sensitivity and fluorescence suppression for epithelial tissue measurements. Laser excitation at 830nm was demonstrated to be optimum. High quality (SN ratio 15-20) NIR-Raman spectra have been acquired from oesophageal and laryngeal tissues in time scales under 30 seconds. Pathological groupings covering the full range of normal and neoplastic tissues in the organs of interest have been studied. Both fresh (snap frozen) and formalin fixed tissue samples were investigated, firstly to indicate whether tissue-types can be distinguished in vivo and secondly to demonstrate the use of Raman spectroscopy as a tool for classification in the pathology lab. Results using multivariate statistical techniques to distinguish between spectra from specimens exhibiting different tissue pathologies have been extremely promising. Cross-validation of the spectral predictive models has shown that three groups of larynx tissue can be separated with sensitivities and specificities of between 86 and 90% and 87 and 95% respectively. Oesophageal prediction models have demonstrated sensitivities and specificities of 84 to 97% and 93 to 98% respectively for a three-group consensus model and 73 to 100% and 92 to 100% for an eight-group consensus model. Epithelial tissues including stomach, tonsil, endometrium, bladder and prostate have been studied to identify further tissues where Raman spectroscopy may be employed for detection of disease. Spectra were similar to those obtained from oesophagus and larynx, although sufficiently different for distinct discriminant models to be required. This work has demonstrated the generic nature of Raman spectroscopy for the detection and classification of cancers and pre-cancerous lesions in many tissues. The evidence provided by this study indicates that utilisation of Raman spectroscopy for non-invasive detection and classification of disease is a distinct possibility. Potential difficulties in the transferability from in vitro to in vivo have been evaluated and no significant barriers have been observed. However, further in vivo probe development and optimisation will be required before 'optical biopsy' with Raman spectroscopy can become a reality.

The uterosacral ligaments (USLs) are important anatomical structures that support the uterus and apical vagina within the pelvis. As these structures are over-stretched, become weak, and exhibit laxity, pelvic floor disorders such as pelvic organ prolapse occur. Although several surgical procedures to treat pelvic floor disorders are directed toward the USLs, there is still a lot that is unknown about their function. These surgeries often result in poor outcomes, demonstrating the need for new surgical approaches and biomaterials. The first chapter of this dissertation presents a review of the current knowledge on the mechanical properties of the USLs. The anatomy, microstructure, and clinical significance of the USLs are first reviewed. Then, the results of published experimental studies on the {emph{in vivo}} and {emph{ex vivo}}, uniaxial and biaxial tensile tests are compiled. Based on the existing findings, research gaps are identified and future research directions are discussed. The second chapter proposes the use of planar biaxial testing, digital image correlation (DIC), and optical coherence tomography (OCT) to quantify the deformations of the USLs, both in-plane and out-of-plane. Using virgin swine as an animal model, the USLs were found to deform significantly less in their main direction (MD) of {emph{in vivo}} loading than in the direction perpendicular to it (PD) at increasing equibiaxial stresses. Under constant equibiaxial loading, the USLs deformed over time equally, at comparable rates in both the MD and PD. The thickness of the USLs decreased as the equibiaxial loading increased but, under constant equibiaxial loading, the thickness increased in some specimens and decreased in others. The third chapter presents new experimental methods for testing the {emph{ex vivo}} tensile properties of the uterosacral ligaments (USLs) in rats. USL specimens were carefully dissected to preserve their anatomical attachments, and they were loaded along their main {emph{in vivo}} loading direction (MD) using a custom-built uniaxial tensile testing device. This chapter reports the first mechanical data on the rat USLs in isolation from surrounding organs. It is also the first experimental study to provide measurements of the inhomogeneous deformations of the USLs during loading along their main textit{in vivo} loading direction, revealing that the USLs may behave as auxetic structures. The fourth and final chapter presents preliminary findings on novel imaging applications to characterize the evolving structure of the USLs before, during, and after tensile pulling along the ligaments' main textit{in vivo} axis of loading. Rat USLs were excised using the proposed novel dissection method and pulled uniaxially as was performed in the previous chapter. Before and after mechanical testing, second harmonic generation (SHG) was used to image collagen and muscle within the three anatomical regions of the USLs. During mechanical testing, OCT was used to collect out-of-plane images of the cervical/intermediate regions of the USL specimens, resulting in 3D volume scans of the regions. SHG images showed the USLs to have complex microstructures with significant wavy collagen bundles interwoven with muscle bundles. Preliminary observation of the microstructure during testing revealed interwoven sections of tissue with collagenous fibers that reoriented in all directions illustrating how the USLs may expand laterally during uniaxial loading, causing the auxetic properties documented in the previous chapter. Though more quantitative work remains to be done, the findings presented in this dissertation improve our understanding of how the USLs deform with increasing load, such as what occurs during pregnancy. Together, these studies serve as a springboard for future investigations on the supportive function of the USLs in animal models by offering guidelines on testing methods that capture their complex mechanical behavior.

Computer vision is a powerful tool for automating the characterization of biological specimen morphology. Classical morphometric studies have provided crucial insights into the skull anatomy of commonly used wildtype (WT) laboratory mice strains such as the C57BL/6. With the increasing use of transgenic (TG) animals in neuroscience research, it is important to determine whether the results from morphometric studies performed on WT strains can be extended to TG strains derived from these WT strains. In this thesis, we first report a new computer vision-based analysis pipeline for surveying mouse skull morphology using Microcomputed Tomography (µCT) scans. We applied this pipeline to study and compare eight cohorts of adult mice from two strains, including both male and female mice at two age points. We found that the overall skull morphology was generally conserved between cohorts, with only 13% of landmark distance differences reaching statistical significance. In addition, we surveyed the dorsal skull bone thickness differences between cohorts. We observed significantly thicker dorsal, parietal, and/or interparietal bones in WT, male, or older mice for 53% of thickness comparisons. Many neuroscience experiments require penetrating the mouse skull to record or modulate neural activity in the brain. Craniotomy procedures on sub-millimeter thick skull tissue are time-consuming to perform manually and require substantial training to attain an acceptable success rate. Previous researchers have used automation to reduce the training needed, increase speed, and minimize variability, but insufficient knowledge of the dorsal skull thickness limits their performance. We thus present a fast, non-invasive method which employs preoperative Optical Coherence Tomography (OCT) imaging to guide a robot to perform single-pass craniotomies in mice. The mouse skull is scanned with an OCT scanner immediately prior to surgery, then a custom computer vision-based analysis pipeline extracts an approximately 10 µm axial by 20 µm lateral resolution 3D profile of the dorsal and ventral surfaces of the mouse calvaria within the Field of View (FOV). A cutting path is generated based on the depth of the ventral surface along the desired craniotomy path. Comparison with µCT skull thickness data and preliminary surgery results indicates that this method provides an acceptable profile across most of the mouse dorsal skull, though more iteration is required to ensure accurate measurement of the area around the lambdoid sinus.

No current imaging technology can directly and without significant distortion visualize the defining microscopic features of the human brain. Ex vivo histological techniques yield exquisite planar images, but the cutting, mounting and staining they require induce slice-specific distortions, introducing cross-slice differences that prohibit true 3D analysis. Clearing techniques have proven difficult to apply to large blocks of human tissue and cause dramatic distortions as well. Thus, we have only a poor understanding of human brain structures that occur at a scale of 1–100 μm, in which neurons are organized into functional cohorts. To date, mesoscopic features which are critical components of this spatial context, have only been quantified in studies of 2D histologic images acquired in a small number of subjects and/or over a small region of the brain, typically in the coronal orientation, implying that features that are oblique or orthogonal to the coronal plane are difficult to properly analyze. A serial sectioning optical coherence tomography (OCT) imaging infrastructure will be developed and utilized to obtain images of cyto- and myelo-architectural features and microvasculature network of post-mortem human brain tissue. Our imaging infrastructure integrates vibratome with imaging head along with pre and post processing algorithms to construct volumetric OCT images of cubic centimeters of brain tissue blocks. Imaging is performed on tissue block-face prior to sectioning, which preserves the 3D information. Serial sections cut from the block can be subsequently treated with multiplexed histological staining of multiple molecular markers that will facilitate cellular classification or imaged with high-resolution transmission birefringence microscope. The successful completion of this imaging infrastructure enables the automated reconstruction of undistorted volume of human tissue brain blocks and permits studying the pathological alternations arising from diseases. Specifically, the mesoscopic and microscopic pathological alternations, as well as the optical properties and cortical morphological alternations of the dorsolateral prefrontal cortical region of two difference neurodegeneration diseases, Chronic Traumatic Encephalopathy (CTE) and Alzheimer’s Disease (AD), were evaluated using this imaging infrastructure.

Background Clinical assessment of intermediate age-related macular degeneration (iAMD) is currently focused upon outer retinal structure, despite implicit understanding of potential retina-wide structural and functional impairment owing to inter- neuronal, synaptic, and vascular connectivity. By design, these retinal elements form distribution patterns which are then altered in disease. Thus, application of unsupervised data classification, i.e., cluster analysis, to retinal outcomes, could highlight patterns of pathologic change, directing attention towards retinal elements susceptible in AMD. Aims This thesis aims to map retinal structural and functional changes in iAMD, by applying cluster analysis to localised optical coherence tomography (OCT), OCT angiography (OCTA), and visual field outcomes. Methods Localised retinal OCT thickness across each neuronal/synaptic layer, OCTA vessel perfusion across each vascular complex, and sensitivity across the visual field of iAMD and normal eyes were extracted, then classified into distinct clusters with intra-cluster similarity and inter-cluster separability. Clusters were de-convoluted into topographic maps, revealing spatial patterns of potential retinal changes in iAMD. Results Cluster analysis was validated for retinal topographic mapping, displaying more spatial detail and less variability than standard spatial analyses. After refining lateral resolution of the maps, patterns of structural differences between iAMD and normal eyes were observed to span throughout the entire macula between each neuronal/synaptic layer and vascular complex, while corresponding functional differences extended even further beyond. Patterns commonly exhibited central and superior bias, resembling distributions of normal retinal anatomy, pathoanatomy, and pathophysiology. Large effect sizes underpinned the potential clinical utility of cluster analysis for OCT, OCTA, and visual fields, strengthened by systematic reviews validating mesopic visual field testing for AMD. Conclusion Structural and functional patterns of iAMD impairment span the entire macula, between retinal neuronal/synaptic layers, vascular complexes, and across the visual field. Thus, current clinical focus upon outer retinal structure inadequately reflects total retinal integrity in iAMD. Application of cluster analysis to clinical diagnostic testing of iAMD (including mesopic visual fields) can highlight and direct attention towards susceptible retinal elements in AMD.

This thesis provides a comprehensive summary of my PhD studies, investigating the potential application of diverse laser technologies in treating two prevalent eye conditions: glaucoma and meibomian gland dysfunction (MGD). Glaucoma is the leading cause of irreversible blindness affecting approximately 80 million individuals worldwide. We explored the use of femtosecond lasers for precise photodisruption of the trabecular meshwork, a vital surgical region within the human eye. The dissertation begins with an examination of the optimization of pulse energy levels in femtosecond laser trabeculoplasty (FLT), enhancing its effectiveness as a treatment for glaucoma. Additionally, the temperature variations observed during FLT surgeries and evaluation of potential collateral damage in human cadaver eyes have been investigated. To enhance targeting precision in surgical interventions, we have developed a micron-scale spectral domain optical coherence tomography system tailored for iridocorneal angle imaging. The thesis highlights the use of short-time Fourier transform to compensate for dispersion, a crucial step in achieving superior axial resolution. Moreover, advanced imaging processing techniques and hardware implementations are presented to demonstrate the comprehensive and detailed visualization of the surgical area within the angle. In the second part of the dissertation, attention is shifted towards our research endeavors focused on addressing MGD. Firstly, methods leveraging numerical modeling and analytical derivations are discussed, shedding light on alternative mechanisms underlying the development of obstructive MGD. Additionally, an innovative treatment approach called selective photothermal ablation (SPA) is introduced, showcasing its potential in selectively targeting the meibomian glands while preserving the overlying conjunctival integrity.

The transparent outer layer of the eye, known as the cornea, has a vital function inbending and directing light onto the retina, which is essential for achieving clear vision. Current methods of correcting refractive errors that are becoming increasingly popular include LASIK and PRK surgeries; however, these invasive techniques come with downsides as well such as permanent thinning of the cornea. This thesis proposes the use of a non-invasive technique called electromechanical reshaping (EMR) that can be applied to the cornea to induce curvature change. EMR was performed on New Zealand white rabbit globes using a concave platinum lens as the working electrode in a 3-electrode setup. The primary outcomes to be measured include the aforementioned curvature change of the cornea and the change in distribution of collagen orientation: to observe such changes the advanced imaging modalities of optical coherence tomography (OCT) and second harmonic generation (SHG) have been employed. The curvature data can be analyzed through a developed MATLAB approach that reconstructs the 3D surface of the cornea from 2D cross-sectional OCT images and sphere-fits the surface to extract the radius of curvature. The collagen structural change can be analyzed in FIJI software using OrientationJ to quantify the orientation of collagen fibers. These methods serve as a sound quantitative way to analyze the outcomes of EMR. This thesis found that the mean curvature increased from 5193.73 µm ± 597.09 µm to 5429.16 µm ± 736.08 µm following EMR application. Regarding collagen structural change, most of the eyes did not show a statistically significant difference following EMR application. Due to experimental error because of the lack of standardization of pressure, however, the corneal curvature did not consistently increase and the corneas did not resemble the radius of curvature of the platinum lens used in EMR (7.486 mm). Future directions include standardization of the pressure applied on the cornea by the platinum lens, simultaneous OCT imaging during EMR application, seeing if corneas post-EMR retain curvature changes, and transitioning to applying EMR on eyes intact in New Zealand white rabbit heads.

Congenital heart disease (CHD) is the most common birth defect and the leading cause of infant death. The mechanisms behind CHD have been the focus of many studies but our understanding of CHD causes still remains incomplete. One reason for this is the lack of appropriate tools for investigating cardiac functions in early embryonic hearts. Our group and others have adapted optical coherence tomography (OCT) in embryonic cardiology research to investigate both structure and hemodynamics of embryonic hearts, because of its high spatial resolution, fast speed, and non-invasiveness. Optical mapping (OM) is a powerful tool for imaging cardiac electrophysiology and was recently improved by our group for studying avian embryonic hearts. One work presented in this dissertation investigated the effects of prenatal ethanol exposure on cardiac conduction using OM and OCT. Our results showed that ethanol-treated embryos developed faster conduction at the atrioventricular junction than controls. Still, this alteration in conduction was not strictly correlated with the reduction in cushion size. To understand the mechanism of this conduction alteration, registering the measurements from structural OCT, Doppler OCT, and OM is needed for an integrated analysis of heart structure, hemodynamics, and conduction in individual embryonic hearts. Measuring using OCT images requires segmentation of cardiac structures. Manual segmentation used in previous studies is time-consuming and hampers high-throughput analysis. Here we present two deep-learning-based techniques to achieve the automatic segmentation of cushion structures from volumetric OCT images and the semi-automatic segmentation of cardiac tissues of a beating heart from 4D OCT images. The segmented heart structures can be the input for analyzing 4D absolute blood flow and endocardial shear stress through a heart cycle. By a sequential scanning of multiple planes of an embryonic heart, OCT provides volumetric measurements of the intact heart. However, conventional OM projects signals from a 3D heart surface to a 2D map, which brings challenges for registering OCT and OM images and causes errors in measuring conduction velocity (CV). To overcome this limitation of OM, our group has proposed a volumetric OM system based on the light-sheet microscope. Here we present a 3D measurement of CV from images captured by this OM system. The techniques presented in this dissertation allow high-throughput measurements of heart structure and function, which facilitates future studies investigating the effects of teratogens, such as ethanol or nicotine, on heart development. These studies usually require many samples for comparison across multiple cohorts. In addition, the 3D measurements of individual hearts provided by OCT and OM could be directly registered to enable a spatial correlation of structural, functional, and molecular aspects in embryonic hearts and facilitate a better understanding of the interplay between these factors during heart development.

INTRODUCTION: Schizophrenia (SZ) and bipolar disorder (BD) are neurodegenerative psychiatric disorders characterized by psychosis, cognitive impairment, and grey- and white-matter reductions in the brain. Non-invasive optical coherence tomography (OCT) has been increasingly utilized to investigate retinal abnormalities and their connections with underlying pathophysiology of psychiatric disorders. This thesis is a meta-analysis of current literature examining differences in retinal cytoarchitecture measured with OCT in patients with psychosis compared to controls. METHODS: In this meta-analysis, 38 articles were identified using PubMed and Google Scholar. Diagnostic groups were SZ only, BD only, psychosis spectrum disorder (PSD) only, psychosis proband (SZ, BD, and PSD combined), and healthy control (HC) eyes. Meta-analyses utilized fixed and random effects models when appropriate, and publication bias was identified and corrected for using trim-and-fill analysis. Meta-analyses and meta-regressions were with the ‘meta’ package in R (version 4.1.1). Results were reported as standardized mean differences (SMD) with 95% confidence intervals. RESULTS: A total of 3065 patient eyes (1664 SZ, 1189 BD, 212 PSD) and 3053 HC eyes were included in this meta-analysis. Compared to HCs, significant reductions were found in overall peripapillary RNFL thickness in BD and macular total retinal and mGCC thicknesses in proband, SZ, and BD groups. Overall, temporal, and inferior pRNFL thickness was significantly lower than controls in all patient groups except SZ, while superior and nasal pRNFL thickness was significantly lower than controls in proband and BD groups. Smaller significant reductions were also found in MV (except BD), mGCL-IPL volume, mGCL-IPL thickness (except BD), and foveal thickness (probands and PSD only). Finally, significant increases were seen in mOPL thickness (probands and PSD) and mINL volume (BD only). CONCLUSION: This meta-analysis builds upon previous literature in this field by incorporating recent OCT studies and examining both peripapillary and macular retinal regions with respect to psychotic disorders. Overall, this meta-analysis demonstrated both peripapillary and macular structural retinal abnormalities in people with psychosis compared to healthy controls. Specifically, the pRNFL, mGCC, and macular total retina thicknesses were widely shown to be decreased in association with psychosis.

Diabetes is a condition affecting 7.4% of Australians. Individuals with diabetes often develop complications, which include retinopathy, neuropathy, and kidney disease. Consequently, these individuals require multidisciplinary care. The provision of accessible and timely care is critical, especially with retinopathy, where eye examinations are required to prevent and delay visual impairment. Thus, the objective of the thesis was to assess the current standard of eye care and investigate new ways to enhance eye care for individuals with diabetes. This was explored over two sections. The first section comprised of three studies to explore current models and examine the efficacy of new models. The first study investigated wait lists at a public hospital ophthalmology clinic through a review of referrals. This study established that wait lists were encumbered by poorly targeted referrals for chronic ocular conditions, which could potentially delay access to eye care for individuals with diabetes. Subsequently, two studies were conducted to assess changes in access from two recently implemented models. The second study comprised of a randomised clinical trial that evaluated a metropolitan public hospital collaborative optometry-ophthalmology clinic. Low‑risk participants with diabetes examined by an optometrist experienced quicker wait times without affecting diagnostic accuracy. The third study evaluated a nationwide diabetic retinopathy screening programme operated at primary health care facilities. A survey of health care practitioners, and audit of photos graded by an optometry-led service revealed an increase in access to retinopathy screening. Evaluation of these models revealed that optometrists play a vital role in providing alternative pathways, and that the models improve access in both urban and non‑urban regions. The second section of the thesis comprised of two experimental studies investigating new uses of corneal confocal microscopy and optical coherence tomography which visualise the corneal nerves and retinal layers, respectively. Two cross-sectional studies were conducted to examine corneal and retinal changes in individuals with diabetes. These studies indicated reductions in corneal nerve morphology and retinal layer thicknesses. Since optometrists are familiar with these devices, there is potential to enhance eye examinations in the future by utilising these ocular imaging instruments to detect other diabetic complications.

Dental caries is one of the most prevalent chronic diseases affecting populations worldwide. With the prevalence of tooth-matched restorative options, the occurrences of recurrent and secondary caries have dramatically increased due to leakage in the interfaces between restorative materials and tooth structure, allowing fluid and bacterial acid infiltration. It is not sufficient to simply detect carious lesions; methods are needed to assess the activity of the lesion and determine if chemical or surgical intervention is necessary. Previous studies have demonstrated the potential of non-ionizing optical imaging technologies for the early detection and diagnosis of lesion severity and depth. The purpose of my project is to quantify the structural differences between active carious and arrested lesions using optical imaging methods. The goal is to provide imaging methods to better assess lesion activity to avoid unnecessary surgical intervention and to allow safe routine monitoring of dental caries without radiation exposure. All carious lesions have a surface layer due to the occurrence of some redeposition of mineral during lesion formation. For arrested lesions, the surface layer has a much higher mineral content due to additional mineral deposition during remineralization, which leads to decreased permeability of fluids including water and plaque generated acids. The higher mineral content can approach that of sound tissues and can produce a zone that appears more transparent to visible, near-IR and SWIR light, called a transparent surface zone. Previous in vitro and in vivo studies on enamel and root surfaces have shown that the thickness of this transparent surface zone can be measured nondestructively using optical coherence tomography (OCT). Other studies also have demonstrated that short-wave infrared (SWIR) reflectance and thermal imaging coupled with dehydration can be used to measure changes in the permeability of lesions in enamel and dentin. However, it has not been established how thick the surface zone should be to inhibit the penetration of these fluids. In these studies, SWIR reflectance and thermal imaging during dehydration with forced air were used to measure changes in the permeability of lesion structure. SWIR imaging at 1400-2300 nm wavelengths coincides with higher water absorption and exploits the increased contrast caused by loss of water from porous lesion areas. Thermal imaging at 6-10 μm wavelengths is sensitive to changes in temperature on tooth surfaces produced by water evaporation from porous lesion areas during dehydration. SWIR reflectance and thermal imaging were used to image simulated enamel and dentin lesions, primary coronal lesions on extracted teeth, and secondary lesions on extracted teeth. The lesions were also assessed by optical coherence tomography (OCT) and correlated with dehydration rates to determine lesion activity. Micro-computed tomography (MicroCT) was used to further confirm lesion severity and structure. The results from these studies suggest that the relationship between surface layer thickness and lesion permeability is highly non-linear, but significantly negatively correlated. A small increase in the surface layer thickness may lead to a significant decrease in permeability. Increasing transparent surface layer thickness led to decreased permeability of lesions, potentially indicating an arrest in activity at thicknesses exceeding 70 μm. Permeability measurements performed best on smooth surface lesions. Based on these results, custom handheld probes employing SWIR, thermal, and OCT imaging were fabricated for small feasibility studies for in vivo assessment of lesion activity in patients. Infrared imaging may significantly improve caries diagnosis and management. These technologies are suitable to produce portable handheld instruments to detect and monitor decay without ionizing-radiation and to increase dental outreach globally.

Optical microscopy has had a revolutionary impact in the biomedical sciences. Among other modalities, optical coherence tomography (OCT) offers a unique capability for label-free structural imaging of biological systems at cellular resolution over millimeter-scale volumetric field-of-view. The rapidly growing field of mechanobiology has presented immense opportunities for not only structural microscopy, but also functional imaging of biomechanical properties with emerging optical elastography techniques. Importantly, attention has been given to the role of biomechanical interactions between cells and the extracellular matrix (ECM) in various biological processes, including onset and progression of cancer, stem cell differentiation, morphogenesis, and wound healing. Although a suite of techniques is available for both biochemical and biophysical characterization of the cells, techniques for mechanical characterization of the ECM are still typically limited to surface micro-indentation via atomic force microscopy (AFM) or bulk mechanical testing. This drives the need for new imaging tools to probe spatially-resolved micromechanical properties of the ECM at the cellular scale in the physiologically relevant 3D environments. Indeed, the enhancement of spatial resolution has been an ongoing pursuit in all fields of imaging. The first portion of this dissertation presents the development and demonstrations of photonic force optical coherence elastography (PF-OCE), a new optical elastography technique to enable quantitative 3D micromechanical microscopy of biopolymer constructs and engineered cellular systems. PF-OCE utilizes long-range optical micromanipulation with radiation pressure from a weakly-focused laser beam to achieve an ‘AFM-like’ localized “pushing” of micro-beads embedded and distributed in 3D space within the sample. The second portion of this dissertation addresses fundamental questions related to the factors that limit spatial resolution and approaches for resolution enhancement in both elastography and optical coherent imaging. As a whole, this dissertation contributes technological advances in the field of optical elastography that offer new imaging capabilities to support future mechanobiological research endeavors as well as new perspectives and implications related to the fundamental imaging science of spatial resolution in both elastography and optical coherent imaging.

The quality of tissue images recorded by optical devices is highly related to the beam profile in the tissue. However, the beam profile is distorted in the tissue due to scattering and non-ideal lens. Offset optical coherence tomography, OCT, technology is introduced to reconstruct beam profile in the tissue. The sample arm detector is moved transversely to the detected offset signal in offset OCT. The OCT detected signal is carried by the photons that are reflected in the overlapping area of the illumination beam and detection area based on the single scattering model. Therefore, a sectional image of the beam profile in tissue is recorded at every offset position. The combination of all offset images reconstructs the beam profile in tissue. Then the property of beam is obtained by equation fitting, such as focus position and beam waist. Knowing the beam profile in the tissue can enhance image quality and broaden the applications of other devices, such as adaptive optics.

In dentistry optical coherence tomography (OCT) technology has shown some promise as a method to distinguish between enamel, dentin, and restorative materials of tooth specimens. Ultrasound (US) technology has been reported with applications in dentistry to image deep tissues which offers a means to further characterize various soft tissue anomalies. While it is believed that both US and OCT technologies have real-time imaging potential for dentistry, their ability to visualize multiple types of simulated defects within root canal systems has yet to be tested. This study was setup to help determine the efficacy of two catheter-based imaging probes in prepared root canals containing areas of interest. Areas of interest herein are cited as vertical fracture lines, simulated perforations, resorptive-like defects, sites of intact dentin, and void space variance of the lumen. 33 human teeth were selected and underwent root canal analysis using 2 commercially available intravascular catheter-based imaging probes integrated with either OCT or US technology. This study proved that intravascular OCT is a very powerful imaging modality capable of (1) detecting various areas of endodontic interest, (2) yielding superficial imaging data of root canal architecture, and (3) trans-imaging tooth specimens from the canal lumen to the external surface of intact teeth at various cross-sections. Intravascular US probe was not capable of producing useful imaging data per the methodology herein. To date there are no FDA approved OCT probes commercially available for use in endodontics. Hopefully this study furthers our understanding of how useful and multimodal OCT technology truly is.

Photobiomodulation (PBM) therapy involves the irradiation of tissues with red to near- infrared (NIR) light at low power densities to stimulate healing, reduce inflammation, and promote optimal cellular functioning. These beneficial effects are thought to occur due to the absorption of NIR light by the chromophore, and terminal enzyme in the mitochondrial electron transport chain, cytochrome c oxidase (CCO). It is hypothesized that increased oxygen consumption due to the photostimulation of CCO, as well as photodissociation of the vasodilator nitric oxide from its binding site in the binuclear center of CCO, contribute to improved tissue healing by increasing blood flow to the irradiated region. Applied to the brain, PBM therapy has the potential to improve many neurological injuries and diseases for which reduced cerebral blood flow (CBF) is a common finding. This study examines whether cortical irradiation with NIR light has an impact on CBF in mice. Mice were administered brain PBM via 810nm, 190mW LED for 18 minutes. CBF was measured before, during, and after treatment using Doppler Optical Coherence Tomography. Results from 16 trials demonstrated a significant, 40% increase in CBF during NIR treatment. This CBF increase was not observed during control trials. Additionally, irradiation with a 730nm LED did not increase CBF, indicating that the blood flow increase observed with 810nm irradiation was not simply due to tissue heating. These findings provide support for the value of PBM therapy for the treatment of neurological conditions.

INTRODUCTION: Schizophrenia (SZ) and bipolar disorder (BD) are neurodegenerative psychotic disorders hallmarked by reductions in gray and white matter volume. Limitations in neuroimaging have led to the use of OCT to study retinal layer biomarkers and their relation to brain pathology. This thesis includes a meta-analysis of current literature and an exploratory analysis of retinal layer thickness in relation to SZ and BD. METHODS: For the meta-analysis, twelve articles were identified using PubMed, Web of Science, and Cochrane database. Diagnostic groups were proband (SZ and BD combined), SZ only, BD only, and healthy control (HC) eyes. Analyses utilized fixed and random effects models, in addition to assuring that bias was adjusted for and that results were cross-validated. Statistical analyses were performed using the “meta” package in R, with results reported as standard mean differences (SMD). The exploratory analysis included a total of 38 subjects (24 probands and 14 HC). Retinal measures were co-varied for age, sex, race, body mass index (BMI), and best-corrected visual acuity (BCVA). Correlations between retinal and clinical and cortical measures were also performed. Clinical data included illness duration, symptom severity, antipsychotic dosage, and smoking status. Neuroimaging data included gray matter (GM) thickness, gray matter volume, and intracranial volume (ICV). Linear effects and mixed effects models were used to study mean eye and right/left eye measures, respectively. Statistical analysis was done in R. RESULTS: A total of 820 patient eyes (541 SZ and 279 BD) and 904 HC eyes were used for the meta-analysis. Compared to HC eyes, probands, SZ, and BD eyes showed significant thinning the peripapillary retinal nerve fiber layer (RNFL), with atrophy greatest in the nasal, temporal, and superior regions. In addition, all diagnostic groups demonstrated significant reductions in the combined ganglion cell layer and inner plexiform layer (GCL-IPL) compared to HC. No significant differences were found for choroidal and macular measures. No significant relationships were seen from meta-regression analysis for clinical measures. For the exploratory analysis, retinal measures from a total of 24 probands (18 SZ and 6 BD) and 14 HC was studied. Compared to HC, probands showed reductions in overall RNFL in mean eye measures, while increases in the inner and outer RNFL were seen in left eye measures. No significant group differences were seen in the GCL, IPL, and inner nuclear layer (INL). The outer plexiform layer (OPL) showed significant thickening in probands and SZ compared to HC for all eye measures. Probands showed trending reductions in the outer nuclear layer (ONL) in the left eye compared to HC. No significant correlations were found between retinal layers and illness duration, overall PANSS (Positive and Negative Syndrome Scale) score, PANSS negative symptom subscore, and smoking status. PANSS positive symptom subscore showed significant and trending negative correlations to the RNFL and GCL, respectively. Antipsychotic medication dosage displayed a trending negative relationship with the IPL. GM thickness showed a significant and trending negative correlation to the RNFL and ONL, respectively. Furthermore, a trending inverse relationship was observed between GM volume and the OPL. Finally, ICV demonstrated a trending and significant negative relationship with GCL and OPL thickness, respectively. CONCLUSION: The meta-analysis showed that atrophy in RNFL and GCL-IPL measures are widely associated with psychosis. Furthermore, it supports previous findings of gray and white matter reductions in SZ and BD. The exploratory analysis showed psychosis-associated reductions in the RNFL and ONL layers, consistent with previous literature. Contradictory findings, the thickening of the ONL, can be attributed to the conflicting findings, but might also be explained by neuro-inflammatory pathways related to psychotic disorders.

Multimodality imaging technologies have attracted wide attention in both biological researches and clinical practice. However, the low image signal-to-noise ratio (SNR) and the limited capability to label multiple targets are the major challenges to use multimodality imaging in many in vivo biomedical applications. Due to the homogeneity of current optical imaging contrast agents (such as gold and polymer nanoparticles, and fluorophores), only the overall distribution of the targets can be observed. Precise tracking of the trajectory of each individual target is not possible. Microcavity lasers are emerging technologies that have broad applications in biomedical fields. Owing to the high emission intensity, rich spectral information, and narrow linewidth, microcavity lasers may provide a route to achieve deep tissue imaging with a high SNR and track implanted cells with unique identifiers. In this dissertation, I introduce the development of three applications of microcavity lasers in multimodality imaging: ultrasound modulated droplet lasers, in vivo single immune cell tracking, and longitudinal in vivo stem cell tracking for cell therapy. In contrast to fluorescence-based imaging and labeling, our microcavity laser emission-based technologies have demonstrated distinct advantages with significantly improved SNR, sensitivity, multimodality contrast, and unique spectral information for labeling different cells. For ultrasound modulated droplet lasers, this technology leverages both deep penetration depth and high resolution of ultrasound imaging, and the high SNR, imaging contrast and sensitivity of laser emission. I first demonstrated the ultrasound modulated microdroplet lasers in which the laser emission intensity from the whispering gallery mode (WGM) of a micro oil droplet laser can be enhanced up to 20-fold when the ultrasound pressure reaches a certain threshold. This enhancement in laser emission intensity is reversible when the ultrasound is turned off. Furthermore, the ultrasound modulation of the laser output in the frequency domain was achieved by controlling the ultrasound modulation frequency. Finally, I investigated a potential in vivo application of the ultrasound modulated droplet lasing using phantoms vessels containing human whole blood. For in vivo immune and stem cell tracking, I demonstrated a multimodality imaging technology combining optical coherence tomography (OCT), fluorescence microscopy (FM), and lasing emission labeling to longitudinally track the 3D migration trajectories of individual cells transplanted into the subretinal space in vivo. The CdS nanowire lasers, with the distinct lasing spectra generated from the subtle differences in the Fabry-Perot microcavity, were utilized as unique identifiers to label the cells. With strong optical scattering and fluorescence emission, CdS nanowires also served as OCT and FM contrast agents to indicate the spatial locations of the cells. FM could provide the overall 2D cell distribution pattern, whereas the nanowires internalized by cells provide unique lasing emission spectra for differentiating individual cells. Meanwhile, OCT imaging could provide both 3D retinal structure and spatial locations of the cells. By integrating the capabilities of FM, OCT, and lasing emission labeling, longitudinal 3D tracking of individual cells in the subretinal space in vivo was achieved. Our study opens a door to utilize microcavity lasers and multimodality imaging platforms to improve imaging quality and solve real-world clinical problems. In the future, our technologies can also be adopted to support both biological researches and clinical applications such as deep tissue cell tracking, and understanding of the pharmacodynamics (PD) and pharmacokinetics (PK) of cell-based therapies for a comprehensive evaluation of both safety and efficacy.

Optical Coherence Tomography (OCT) has greatly advanced the diagnosis and management of many retinal diseases by enabling in vivo volumetric structural imaging of the retina with high resolution. Usually, retinal OCT is performed at near-infrared (NIR) wavelengths, limiting both axial resolution and contrast for molecules that play a role in vision. Though NIR OCT defines biomarkers that quantify progression of dry age-related macular degeneration (AMD), NIR OCT cannot yet delineate the finest structural and functional changes that define AMD.Visible light OCT has the ability to delineate these changes by providing high resolution and spectroscopic information that can aid in assessing AMD. The higher axial resolution can observe the retinal pigment epithelium (RPE) and Bruch’s membrane (BM) on a sub-micron scale, potentially expanding our knowledge of AMD progression. The molecular contrast can be used for retinal oximetry of blood vessels and potentially photopigment or melanin densitometry which could portend early AMD. Although visible light OCT holds the promise of micron and even unprecedented sub-micron axial resolution and molecular contrast, visible light OCT systems to date have not delivered on this promise. There are many confounding factors that need to be addressed before the full potential of visible light OCT is realized. These include the cost of hardware, size of imaging system, safety considerations limiting light exposure, excess noise in light sources, motion artifacts, chromatic aberrations, and spatially-dependent dispersion. This thesis advances the development of visible light OCT by addressing all of the previously listed issues. With these advances, we can now clearly visualize additional retinal bands in the mouse (and human) retina such as the RPE, BM, inner plexiform layer (IPL) sublaminae, and the dark band inner to the external limiting membrane (ELM).

Optical Coherence Tomography (OCT) is a depth-resolved, interferometric technique that enables micron resolution, label-free imaging in vivo. OCT is a standard of care in ophthalmology, but has also had an impact in cardiology as well as a number of emerging areas. In OCT, a broadband spectrum facilitates optical depth sectioning by providing a coherence gate. At the same time, this broadband spectrum also provides the ability to decode tissue chromophore content from the differential signal attenuation versus depth. Typically, OCT is performed between 700 nm and 1600 nm. In this thesis, new and emerging OCT “colors,” or wavelength ranges, are investigated through a series of demonstrative studies in mice and rats. The introduction describes relevant considerations for selecting the appropriate OCT color. In the visible light range (Chapter 2), which benefits from high hemoglobin absorption, a novel way of estimating vessel hemoglobin and saturation was proposed. In the 1300 nm optical window (Chapter 3), light-blood cell interaction was investigated in the retina to understand the contrast mechanisms of OCT angiography in the retina. Finally, two emerging colors for OCT were investigated in vivo. In the 1700 nm optical window (Chapter 4), benefitting from minimal overall ballistic light attenuation, cellular resolution deep brain imaging was achieved. In the 2200 nm optical window (Chapter 5), benefitting from even lower scattering and low attenuation in water-scarce tissues, non-invasive in vivo imaging of the brain was achieved for the first time. Conclusions are summarized and future directions are discussed in Chapter 6.

Purpose: The purpose of this study is to observe structural changes and lesion activity of early occlusal pit and fissure caries on primary teeth using CP-OCT. The hypothesis is that CP-OCT will be able to successfully identify the presence of a transparent surface zone of reduced reflectivity that is indicative of remineralization and an arrested lesion.Methods: Participants (n=30 with 61 primary molars) aged 6 to 10 years old participated in the study. All lesions were clinically examined and given a diagnosis according to the ICDAS codes. All lesions were then scanned with CP-OCT. Images were converted and analyzed with image analysis software.Results: OCT scans showed that 57 teeth (93%) had pit and fissure lesions and 4 teeth (7%) were without lesions. Several teeth, n=16 (26%), showed a distinct surface zone that indicated arrested lesions. Most of the teeth, n=45 (74%), did not show evidence of surface zone, indicative of active lesions. Several of the teeth, n=11 (18%), had lesions that were visible with OCT but were not visible in the visual examination.Conclusions: OCT can detect early occlusal caries that cannot be identified on radiographs or through a clinical exam. OCT can provide information on lesion activity by detecting the presence of a transparent surface zone, indicative of lesion arrest, and can precisely show the depth of the lesions. OCT will be a valuable tool in the future that can provide useful information to the clinicians to aid with their diagnosis of early occlusal pit and fissure caries.

Ophthalmic technologies have evolved over the past ten years to not only resolve every photoreceptor within the densely packed fovea, but also to reveal hidden structures within the translucent retinal layers. Although structurally intact, patches of seemingly healthy photoreceptors could have a decreased sensitivity indicating signs of pathology with no structural discrepancies visible. To better understand the health of the retina we have further developed both structural and functional retinal imaging to shed light on the photoreceptors as a more precise indicator of health by probing the sensitivity and physical elongation of these neurons upon stimulation. With a cellular-scale tool which can quantify both the neuron’s structure and function, the health of the retina can be precisely monitored and probed to bring new insights into pathophysiology and diagnostics of retinal diseases.Adaptive optics scanning laser ophthalmoscopy (AOSLO) is a powerful tool for imaging the retina at high spatial and temporal resolution. In this dissertation, four developments are documented based on AOSLO technology for imaging the structure and function of the retina. Firstly, a wide-vergence, multi-spectral AOSLO was designed, constructed, and experimentally verified by measuring the point spread function (PSF) of the illumination and collection paths for each spectral channel via a phase retrieval technique. The system’s optical quality was then demonstrated by resolving the foveal cone mosaic in all three imaging channels from human volunteers and comparing against expected performance. Secondly, a multi-detector scheme for AOSLO with two main detection configurations was developed: pixel reassignment and offset aperture imaging. In the multi-detector scheme, the single element detector of the standard AOSLO was replaced by a fiber bundle which couples the detected light into multiple detectors. The pixel reassignment configuration enabled high resolution imaging with an increased light collection efficiency. The offset aperture imaging configuration enhanced the detection of multiply scattered light, which improves the contrast of retinal vasculature and inner retinal layers. Thirdly, an additional system was built with active eye motion correction for an optical coherence tomography (OCT). The AOSLO was an integral part for driving the aberration correction and tracking the eye motion to guide the AOOCT. An independent focus adjustment was implemented into the AOOCT path for imaging the nerve fiber layers and ganglion cells with optimal lateral resolution while maintaining high fidelity photoreceptor mosaic for AOSLO tracking. Lastly, by using the complex field from measured AOOCT interferogram, the phase information was acquired to measure the physiological response of the photoreceptors with nm scale accuracy and record the elongation of the cone outer segment in response to a stimulus. This system successfully characterized the optoretinogram of photoreceptors which has potential to be further utilized as an optical biomarker for the function of the neuron allowing both the classification of the cone type and the assessment of the photoreceptor’s health.

The application of three-dimensional (3D) tumor spheroids has been expanding due to their ability to closely mimic several features of solid tumors such as their cellular heterogeneity/organization and growth kinetics. Optical Coherence Tomography (OCT) system has been utilized to characterize 3D morphological and physiological information of multicellular tumor spheroids. In order to characterize and analyze the results of 3D OCT spheroid datasets, there is a need to develop an automated algorithm with high accuracy that can calculate the volume of a tumor spheroid and its necrotic tissues. The developed automated algorithm can automatically detect the margin of the 3D tumor spheroids and its necrotic region. The measurements from the automated program were then compared with the manual method to assess the accuracy of the developed algorithm through calculations of the Dice coefficient, and the results show a Dice number of 0.9449 and 0.9145 for spheroid and necrotic volume algorithms, respectively. Additionally, curve fitting was performed to further study the growth kinetics of the spheroid and its necrotic tissues, and measures such as root-mean-square error (RMSE) and corrected Akaike information criterion (AICc) were taken for this assessment. According to the RMSE measure, Boltzmann was the best-fitted model for the overall spheroid volume growth. The logistic model, on the other hand, was best fitted in modeling the growth of necrotic core according to both RMSE and AICc values. Quantification of the spheroid volume (and its necrotic core) is significant as morphological features are often related to tumor activities, and determination of the best model is also vital in predicting the behavior of the spheroids. Overall, the algorithm used for this study allows for more efficient, in both time and accuracy, studies such as evaluating the growth medium’s effect on tumor spheroids, growth characterization of varying cell lines, as well as the efficacy of a certain drug.

Cancer is a complex disease that is often tissue and context dependent. Tumor microenvironment has been shown to have pivotal roles in regulating tumor initiation, growth and metastasis. Enrichment of cancer associated fibroblasts (CAFs) have been shown to promote cancer cell invasion by modulating physiochemical components of ECM, promoting angiogenic behaviors of endothelial cells (ECs) and shuffling metabolites to satisfy tumor metabolic demands. Obesity worsens the prognosis for breast cancer patients, and adipose stromal cells (ASC)-mediated fibrotic ECM remodeling of breast tissue plays a role in this process. Obese ASCs have been shown to share many similarities to CAFs. Whether or not obese vs. lean ASCs differentially affect the other factors important to progression of premalignant breast cancer, remains unclear. In this dissertation, I proposed the hypothesis that obese vs. lean ASCs can prime the breast tissue microenvironment to be permissive to breast cancer progression by remodeling the surrounding extracellular matrix (ECM), altering angiogenesis and reprogramming metabolism. Leveraging different tissue engineering strategies, I designed numerous physiologically relevant 3D in vitro models and developed advanced imaging tools to investigate 1) how does obese ASC and ECM remodeling mediate breast cancer cell invasion? 2) how does ASC and ECM remodeling contribute to angiogenesis? 3) what is the metabolic interplay between ASC and tumor cells during cancer invasion? Results from these studies suggest that 1) direct cell-cell contact with ASCs enables collective tumor cell migration and obese ASCs are more effective than their lean counterparts. Both matrix metalloproteinase-dependent proteolytic activity and ASC contractility are important during obese ASC mediated collective cancer migration. 2) Obese ECMs promote the proangiogenic behavior of ECs by altering their proliferative, secretory, and invasive capacities as compared to lean ECMs. 3) A label free multiphoton anisotropy imaging platform can be used to measure NAD(P)H dynamics as an indirect readout for cell metabolism. Combining with gold standard seahorse analysis, it is a powerful tool to allow us to monitor the metabolic states of ASCs and tumor cells in various culture platforms. In summary, tools and models developed in this dissertation provide novel insights into how different aspects of obesity associated microenvironmental changes are functionally related to breast cancer cell invasion, which increase the understanding of how obesity promotes breast cancer.

Mechanobiology is a prominent research field which seeks to elucidate the role of physical forces and mechanical interactions throughout various biological processes, including morphogenesis, wound healing, and cancer metastasis, among others. Traction force microscopy (TFM) is an important family of experimental techniques used by mechanobiologists to study and quantify the forces that cells exert upon their surroundings. Recent years have seen a growing demand for TFM methods capable of studying the dynamic, 3D, and collective behaviors of cells embedded within optically scattering media. However, traditional imaging modalities for TFM (e.g., confocal microscopy) do not currently allow researchers to satisfy these demands. In this dissertation, I present traction force optical coherence microscopy (TF-OCM), a TFM platform based on optical coherence tomography (OCT), to address the as yet unmet imaging needs of mechanobiology researchers and study the dynamic mechanical behavior of cells and multicellular collectives within scattering media. In the first half of this dissertation, I summarize current methods and emerging needs of the TFM field and provide detailed derivations and discussions regarding signal processing methods for OCT imaging. In the latter half, I present the key experimental findings of my research. A pilot study was first performed to demonstrate the ability of OCT imaging to capture substrate deformations induced by cellular traction forces (CTFs). This was followed by a proof-of-concept study which enabled the quantitative reconstruction of time-varying CTFs exerted by isolated cells, resulting in the realization of TF-OCM as a full-fledged experimental technique. The critical image reconstruction procedures developed along the way have since proven useful in the context of other OCT imaging applications as well. Finally, a collaborative application-focused study was performed, which demonstrated the ability of TF-OCM to study the dynamics of large multicellular collectives embedded within scattering collagen substrates. Although much work remains to be done in order to enable quantitative TF-OCM in such complex settings, these findings show that TF-OCM offers a promising avenue to pursue new and valuable research endeavors in mechanobiology.

Congenital heart disease/defects (CHDs) account for approximately one-third of all birth defects globally. Many of these will require invasive treatment within the first year of life, subsequent interventions, and a lifetime of monitoring. Alcohol has been known as a teratogen for several decades, and prenatal exposure alone is a significant cause of worldwide CHDs.Optical Coherence Tomography (OCT) has been used as an imaging modality for nearly three decades and is especially suited to the non-invasive imaging of small, semi-transparent tissue structures. Doppler OCT (DOCT) adds the ability to visualize and measure fluid flow and movement of reflective components within the tissue.This work presents the development of technology to further enable DOCT as a tool in measuring the function of anatomical structures. First, an interferometer design is described, which significantly reduces phase noise by incorporating a second, narrow band, continuous-wave light source as a phase-reference. By implementing this interferometer and related processing algorithms into a DOCT system, significant frequency noise reduction is demonstrated in reflective and scattering samples.Second, a modification to a DOCT system is presented using a single sample beam that provides velocity information from multiple angles within the beam. By introducing a delay element into part of the OCT beam path, the sample beam is divided into several components, each with a different group delay and each providing a separate interferogram with its own effective Doppler angle. By combining the Doppler shift measured in each of these component interferograms, the flow velocity vector is fully determined.OCT and DOCT are then applied to an embryonic avian model for Fetal Alcohol Spectrum Disorder (FASD) in order to study the effects of alcohol on early heart development. Folic acid is administered to a test group to learn more about its role in preventing CHDs. Through these embryonic studies, this work suggests that measurable changes in early-stage cardiac function could be not only an effect but also a cause of CHDs and that the introduction of substances such as folic acid could play a mitigative role at crucial junctures in cardiogenesis.

The objective of this thesis was to determine if a model to evaluate ocular response to short term exposure with optical defocus could be developed using the parameters of central and peripheral eye length and choroidal thickness. To achieve the objective, the following experiments were conducted: a) identify and improve methods to measure central and peripheral eye length and choroidal thickness and to determine repeatability of methods; b) conduct a provocative test to determine the limits of change of choroidal thickness; c) impose short term optical defocus on human eyes and measure central and peripheral eye length and choroidal thickness as well as accommodative response, and d) study the influence of time of day on eye length and choroidal thickness response to short term optical defocus. Eye length and choroidal thickness measurements were conducted with Lenstar (Haag‐Streit Koeniz, Switzerland) and SS OCT (Topcon, Tokyo, Japan) and a custom attachment for Lenstar was developed to enable peripheral eye length measurements. A 3D volume scan was conducted with OCT and choroidal thickness values extracted. Both central and peripheral retina (nasal, temporal, superior and inferior to 20º periphery, in 10º steps) were measured and repeatability assessed. The study involved 20 human adult participants who were measured twice. At the central retina, repeatability for eye length and choroidal thickness was ±13 μm and ±15μm, respectively. At the peripheral retinal locations, repeatability ranged from ±24 to ±93 μm for eye length and ±9 to ±35 μm for choroidal thickness. To estimate the extent to which the choroidal layer changes in thickness, a provocative test involving a change in body posture from sitting to recumbent position was conducted (n=15, adult participants). Choroidal thickness and intraocular pressure (IOP) were measured with the participant in the sitting position and after a change to a recumbent position. IOP increased by 1.02 ± 1.35 mmHg and choroid thickened by 10.39 ± 50.60 μm. The thickening of choroid was not significant. These data were to serve as benchmark to assess the response to optical defocus. In an experiment involving 22 adult human participants, the effects of 30 minutes exposure to optical defocus (myopic (+3.00 D), hyperopic (-3.00 D) and multifocal (Centre-distance, Plano/+2.50 D)) on central and peripheral eye length and choroidal thickness along both horizontal and vertical field meridians (up to 20º, in 10º steps) were investigated. The accommodative response of the eye was also measured. Each participant attended 3 visits (3 separate days, 07:00 a.m. to 11:00 a.m.) where the right eye was measured before and after 30 minutes of exposure to optical defocus. Immediately post exposure to myopic, hyperopic and multifocal defocus, central and peripheral eye length was mostly shorter (-5±12 μm centrally), longer (+4±14 μm centrally) and shorter (-8±14 μm centrally, p=0.02) respectively. In contrast, central and peripheral choroid mostly thinned (-5±20 μm centrally), thickened (+4±17 μm centrally) and thinned (centrally -1±27 μm) in response to myopic, hyperopic and multifocal defocus respectively (all non-significant). Overall choroidal thickness was 7 μm thinner, 5 μm thicker and 7 μm thinner in response to myopic, hyperopic and multifocal defocus, respectively. Post exposure, there were no significant changes in the accommodative response. The results suggested that variations in eye length and choroidal thickness changes were insignificant, except for central eye length change to multifocal defocus. To determine if there was a diurnal variation in the ocular response to imposed defocus, the effects of 30 minutes exposure to myopic, hyperopic and multifocal defocus in morning and evening on central and peripheral eye length and choroidal thickness was evaluated. Each participant (n=10 adults) attended 3 visits on 3 separate days, each between 5:00 p.m. and 8:00 p.m., where the right eye of the participant was exposed to defocus. Measurements were taken before and immediately after 30 minutes of exposure and compared with the results from the morning visits. Immediately post exposure, both central and peripheral eye length was shorter in response to myopic defocus, (morningevening; centrally, +5±11 μm versus -4±12 μm) and shorter in response to multifocal defocus (morningevening; centrally -19±22 μm versus -9±35 μm), thickened in response to hyperopic defocus (morning>evening; centrally +5±21 μm versus +6±18 μm) and thickened in response to multifocal defocus (morning >evening; centrally 9±28μm versus 4±34μm). Significant of these changes were the eye length changes, only at centre, in response to myopic and multifocal defocus in the evening compared to morning. Therefore, a final experiment was conducted to validate these findings (n=7 adults) and similarly found that central eye length was shorter following exposure to optical defocus in the evening, irrespective of the type of defocus (-11±13μm, -6±16 μm, and -16±19 μm for myopic, hyperopic and multifocal defocus respectively). The data indicates that the central and peripheral eye length reduces(shorter) in response to short term exposure to myopic and multifocal defocus and thus, may be useful to evaluate the ocular responses to defocus. Contrary to predictions that the choroidal response will be in anti-phase to eye length changes, surprisingly, the choroidal changes were small in magnitude (mostly

Each endoscopic imaging technique, including optical coherence tomography, fluorescence, ultrasound, or photoacoustic, has unique features as well as limitations. Presently, since no single technique can provide a complete assessment of biological tissue, such as plaque and colorectal wall, several imaging methods are often performed in sequence to achieve a comprehensive evaluation. While the sequential imaging approach can compensate for limitations of each individual technique, the increased X-ray exposure, procedure length, and associated risks cannot be overlooked. As multiple imaging probes are required, repeated probe insertions to the arteries are required, and the associated costs (e.g., guide wires, sterilization, etc.) also increase significantly. In addition, since data acquisition is performed individually, image co-registration is necessary, which is often performed off-line manually or semi-automatically. Not only is image co-registration a tedious and time-consuming task, it also has limited accuracy due to human error and interobserver variances. Therefore, a technique that can simultaneously perform multiple imaging technologies through a single imaging probe would greatly improve clinical outcomes in clinical applications. Here, we present different kinds of multimodal imaging modalities for cardiology and gastrointestinal tract. In vivo and ex vivo studies using rabbit and rat were performed for system validation. The results show that multimodal technology is able to overcomes the limitations of individual intravascular imaging modality, providing more comprehensive information on morphology and/or composition for better characterization.Since the first demonstration of Doppler OCT in 1997, several functional extensions of Doppler OCT have been developed, including velocimetry, angiogram, and optical coherence elastography (OCE). OCT Angiogram (OCTA) is able to reconstruct the microvasculature by detecting fluctuations in the amplitude and phase of the interference signal induced by moving blood cells and plasma. Here, we developed a 1.7-micron OCT/OCTA system for characterization of skin cancer. The use of the longer wavelength allows for a ~25% improvement in penetration depth as well as better identification of microvasculature in the deeper layers of the skin tissue. The feasibility and performance of our system were tested and validated in vivo in human subjects. The developed 1.7-micron OCT/OCTA system has the capability of providing more structural and vascular information at greater skin depths than previous OCT systems, and it has great potential to bring new insights in diagnosis as well as management of skin cancer.OCE possesses micron-level resolution and an axial displacement sensitivity on the order of a few nanometers and, therefore has become an attractive research tool for ophthalmology, dermatology, cardiology, and oncology. Here, we developed an OCE system, which is able to perform a simultaneous evaluation of elasticity in both cornea and crystalline lens. In vivo rabbit experiments were performed to verify the performance as well as investigate the relationship between elasticity of ocular tissue and intraocular pressure and between elasticity and age. In addition, we developed an ultrahigh sensitivity OCE system using a common-path configuration to further improve the system performance. The system has a phase stability of 4.2 mrad without external stabilization or extensive post-processing, such as averaging. We validated the SS-OCECP performance in a tissue-mimicking phantom and an in vivo rabbit model, and the results demonstrated significantly improved phase stability compared to conventional SS-OCE. The significant improved capability suggests that the developed OCE system has great potential to advance ophthalmic research in disorders affecting the lens and the cornea.