Three-dimensional calibration targets for optical coherence tomography

The recent expansion of clinical applications for optical coherence tomography (OCT) is driving the development of approaches for consistent image acquisition. There is a simultaneous need for time-stable, easy-to-use imaging targets for calibration and standardization of OCT devices. We present calibration targets consisting of three-dimensional structures etched into nanoparticle-embedded resin. Spherical iron oxide nanoparticles with a predominant particle diameter of 400 nm were homogeneously dispersed in a two part polyurethane resin and allowed to harden overnight. These samples were then etched using a precision micromachining femtosecond laser with a center wavelength of 1026 nm, 100kHz repetition rate and 450 fs pulse duration. A series of lines in depth were etched, varying the percentage of inscription energy and speed of the translation stage moving the target with respect to the laser. Samples were imaged with a dual wavelength spectral-domain OCT system and point-spread function of nanoparticles within the target was measured.

Advances in characterisation, calibration and data processing speed of optical coherence tomography systems

This thesis describes advances in the characterisation, calibration and data processing of optical coherence tomography (OCT) systems. Femtosecond (fs) laser inscription was used for producing OCT-phantoms. Transparent materials are generally inert to infra-red radiations, but with fs lasers material modification occurs via non-linear processes when the highly focused light source interacts with the materials. This modification is confined to the focal volume and is highly reproducible. In order to select the best inscription parameters, combination of different inscription parameters were tested, using three fs laser systems, with different operating properties, on a variety of materials. This facilitated the understanding of the key characteristics of the produced structures with the aim of producing viable OCT-phantoms. Finally, OCT-phantoms were successfully designed and fabricated in fused silica. The use of these phantoms to characterise many properties (resolution, distortion, sensitivity decay, scan linearity) of an OCT system was demonstrated. Quantitative methods were developed to support the characterisation of an OCT system collecting images from phantoms and also to improve the quality of the OCT images. Characterisation methods include the measurement of the spatially variant resolution (point spread function (PSF) and modulation transfer function (MTF)), sensitivity and distortion. Processing of OCT data is a computer intensive process. Standard central processing unit (CPU) based processing might take several minutes to a few hours to process acquired data, thus data processing is a significant bottleneck. An alternative choice is to use expensive hardware-based processing such as field programmable gate arrays (FPGAs). However, recently graphics processing unit (GPU) based data processing methods have been developed to minimize this data processing and rendering time. These processing techniques include standard-processing methods which includes a set of algorithms to process the raw data (interference) obtained by the detector and generate A-scans. The work presented here describes accelerated data processing and post processing techniques for OCT systems. The GPU based processing developed, during the PhD, was later implemented into a custom built Fourier domain optical coherence tomography (FD-OCT) system. This system currently processes and renders data in real time. Processing throughput of this system is currently limited by the camera capture rate. OCTphantoms have been heavily used for the qualitative characterization and adjustment/ fine tuning of the operating conditions of OCT system. Currently, investigations are under way to characterize OCT systems using our phantoms. The work presented in this thesis demonstrate several novel techniques of fabricating OCT-phantoms and accelerating OCT data processing using GPUs. In the process of developing phantoms and quantitative methods, a thorough understanding and practical knowledge of OCT and fs laser processing systems was developed. This understanding leads to several novel pieces of research that are not only relevant to OCT but have broader importance. For example, extensive understanding of the properties of fs inscribed structures will be useful in other photonic application such as making of phase mask, wave guides and microfluidic channels. Acceleration of data processing with GPUs is also useful in other fields.

Fiber optically integrated cost-effective spectrometer for optical coherence tomography

A tilted fiber Bragg grating (TFBG) was integrated as the dispersive element in a high performance biomedical imaging system. The spectrum emitted by the 23 mm long active region of the fiber is projected through custom designed optics consisting of a cylindrical lens for vertical beam collimation and successively by an achromatic doublet onto a linear detector array. High resolution tomograms of biomedical samples were successfully acquired by the frequency domain OCT-system. Tomograms of ophthalmic and dermal samples obtained by the frequency domain OCT-system were obtained achieving 2.84 μm axial and 10.2 μm lateral resolution. The miniaturization reduces costs and has the potential to further extend the field of application for OCT-systems in biology, medicine and technology. © 2014 SPIE.

Quantitative optical coherence tomography for characterization of microscopic structures with varying refractive index

In this paper we have done back to back comparison of quantitive phase and refractive index from a microscopic image of waveguide previously obtained by Allsop et al. Paper also shows microscopic image of the first 3 waveguides from the sample. Tomlins et al. have demonstrated use of femtosecond fabricated artefacts as OCT calibration samples. Here we present the use of femtosecond waveguides, inscribed with optimized parameters, to test and calibrate the sensitivity of the OCT systems.

A program to analyse optical coherence tomography images of the ciliary muscle

Purpose: To describe and validate bespoke software designed to extract morphometric data from ciliary muscle Visante Anterior Segment Optical Coherence Tomography (AS-OCT) images. Method: Initially, to ensure the software was capable of appropriately applying tiered refractive index corrections and accurately measuring orthogonal and oblique parameters, 5 sets of custom-made rigid gas-permeable lenses aligned to simulate the sclera and ciliary muscle were imaged by the Visante AS-OCT and were analysed by the software. Human temporal ciliary muscle data from 50 participants extracted via the internal Visante AS-OCT caliper method and the software were compared. The repeatability of the software was also investigated by imaging the temporal ciliary muscle of 10 participants on 2 occasions. Results: The mean difference between the software and the absolute thickness measurements of the rigid gas-permeable lenses were not statistically significantly different from 0 (t = -1.458, p = 0.151). Good correspondence was observed between human ciliary muscle measurements obtained by the software and the internal Visante AS-OCT calipers (maximum thickness t = -0.864, p = 0.392, total length t = 0.860, p = 0.394). The software extracted highly repeatable ciliary muscle measurements (variability ≤6% of mean value). Conclusion: The bespoke software is capable of extracting accurate and repeatable ciliary muscle measurements and is suitable for analysing large data sets.

Cost-effective optical coherence tomography spectrometer based on a tilted fiber Bragg grating

A compact, fiber-based spectrometer for biomedical application utilizing a tilted fiber Bragg grating (TFBG) as integrated dispersive element is demonstrated. Based on a 45° UV-written PS750 TFBG a refractive spectrometer with 2.06 radiant/μm dispersion and a numerical aperture of 0.1 was set up and tested as integrated detector for an optical coherence tomography (OCT) system. Featuring a 23 mm long active region at the fiber the spectrum is projected via a cylindrical lens for vertical beam collimation and focused by an achromatic doublet onto the detector array. Covering 740 nm to 860 nm the spectrometer was optically connected to a broadband white light interferometer and a wide field scan head and electronically to an acquisition and control computer. Tomograms of ophthalmic and dermal samples obtained by the frequency domain OCT-system were obtained achieving 2.84 μm axial and 7.6 μm lateral resolution. © 2014 SPIE.

Measurement of scleral thickness in humans using anterior segment optical coherent tomography

Anterior segment optical coherent tomography (AS-OCT, Visante; Zeiss) is used to examine meridional variation in anterior scleral thickness (AST) and its association with refractive error, ethnicity and gender. Scleral cross-sections of 74 individuals (28 males; 46 females; aged between 18-40 years (27.7±5.3)) were sampled twice in random order in 8 meridians: [superior (S), inferior (I), nasal (N), temporal (T), superior-temporal (ST), superior-nasal (SN), inferior-temporal (IT) and inferior-nasal (IN)]. AST was measured in 1mm anterior-toposterior increments (designated the A-P distance) from the scleral spur (SS) over a 6mm distance. Axial length and refractive error were measured with a Zeiss IOLMaster biometer and an open-view binocular Shin-Nippon autorefractor. Intra- And inter-observer variability of AST was assessed for each of the 8 meridians. Mixed repeated measures ANOVAs tested meridional and A-P distance differences in AST with refractive error, gender and ethnicity. Only right eye data were analysed. AST (mean±SD) across all meridians and A-P distances was 725±46μm. Meridian SN was the thinnest (662±57μm) and I the thickest (806 ±60μm). Significant differences were found between all meridians (p<0.001), except S:ST, IT:IN, IT:N and IN:N. Significant differences between A-P distances were found except between SS and 6 mm and between 2 and 4mm. AST measurements at 1mm (682±48 μm) were the thinnest and at 6mm (818±49 μm) the thickest (p<0.001); a significant interaction occurred between meridians and A-P distances (p<0.001). AST was significantly greater (p<0.001) in male subjects but no significant differences were found between refractive error or ethnicity. Significant variations in AST occur with regard to meridian and distance from the SS and may have utility in selecting optimum sites for pharmaceutical or surgical intervention.

Content-Based Image Retrieval for Computer Tomography Images Using Wavelet Descriptors

An approach to building a CBIR-system for searching computer tomography images using the methods of wavelet-analysis is presented in this work. The index vectors are constructed on the basis of the local features of the image and on their positions. The purpose of the proposed system is to extract visually similar data from the individual personal records and from analogous analysis of other patients.

Improving the economic value of photographic screening for optical coherence tomography-detectable macular oedema:a prospective, multicentre, UK study

Objectives: To determine the best photographic surrogate markers for detecting sight-threatening macular oedema (MO) in people with diabetes attending UK national screening programmes. Design: A multicentre, prospective, observational cohort study of 3170 patients with photographic signs of diabetic retinopathy visible within the macular region [exudates within two disc diameters, microaneurysms/dot haemorrhages (M/DHs) and blot haemorrhages (BHs)] who were recruited from seven study centres. Setting: All patients were recruited and imaged at one of seven study centres in Aberdeen, Birmingham, Dundee, Dunfermline, Edinburgh, Liverpool and Oxford. Participants: Subjects with features of diabetic retinopathy visible within the macular region attending one of seven diabetic retinal screening programmes. Interventions: Alternative referral criteria for suspected MO based on photographic surrogate markers; an optical coherence tomographic examination in addition to the standard digital retinal photograph. Main outcome measures: (1) To determine the best method to detect sight-threatening MO in people with diabetes using photographic surrogate markers. (2) Sensitivity and specificity estimates to assess the costs and consequences of using alternative strategies. (3) Modelled long-term costs and quality-adjusted life-years (QALYs). Results: Prevalence of MO was strongly related to the presence of lesions and was roughly five times higher in subjects with exudates or BHs or more than two M/DHs within one disc diameter. Having worse visual acuity was associated with about a fivefold higher prevalence of MO. Current manual screening grading schemes that ignore visual acuity or the presence of M/DHs could be improved by taking these into account. Health service costs increase substantially with more sensitive/less specific strategies. A fully automated strategy, using the automated detection of patterns of photographic surrogate markers, is superior to all current manual grading schemes for detecting MO in people with diabetes. The addition of optical coherence tomography (OCT) to each strategy, prior to referral, results in a reduction in costs to the health service with no decrement in the number of MO cases detected. Conclusions: Compared with all current manual grading schemes, for the same sensitivity, a fully automated strategy, using the automated detection of patterns of photographic surrogate markers, achieves a higher specificity for detecting MO in people with diabetes, especially if visual acuity is included in the automated strategy. Overall, costs to the health service are likely to increase if more sensitive referral strategies are adopted over more specific screening strategies for MO, for only very small gains in QALYs. The addition of OCT to each screening strategy, prior to referral, results in a reduction in costs to the health service with no decrement in the number of MO cases detected. © Queen's Printer and Controller of HMSO 2013.

Microlocal Approach to Tensor Tomography and Boundary and Lens Rigidity

2000 Mathematics Subject Classification: 53C24, 53C65, 53C21.

The design and validation of an optical coherence tomography-based classification system for focal vitreomacular traction

PurposeTo develop and validate a classification system for focal vitreomacular traction (VMT) with and without macular hole based on spectral domain optical coherence tomography (SD-OCT), intended to aid in decision-making and prognostication.MethodsA panel of retinal specialists convened to develop this system. A literature review followed by discussion on a wide range of cases formed the basis for the proposed classification. Key features on OCT were identified and analysed for their utility in clinical practice. A final classification was devised based on two sequential, independent validation exercises to improve interobserver variability.ResultsThis classification tool pertains to idiopathic focal VMT assessed by a horizontal line scan using SD-OCT. The system uses width (W), interface features (I), foveal shape (S), retinal pigment epithelial changes (P), elevation of vitreous attachment (E), and inner and outer retinal changes (R) to give the acronym WISPERR. Each category is scored hierarchically. Results from the second independent validation exercise indicated a high level of agreement between graders: intraclass correlation ranged from 0.84 to 0.99 for continuous variables and Fleiss' kappa values ranged from 0.76 to 0.95 for categorical variables.ConclusionsWe present an OCT-based classification system for focal VMT that allows anatomical detail to be scrutinised and scored qualitatively and quantitatively using a simple, pragmatic algorithm, which may be of value in clinical practice as well as in future research studies.

Clinical translation of a hand-held optical imager for breast cancer diagnostics: In vitro and in vivo tomography studies

Optical imaging is an emerging technology towards non-invasive breast cancer diagnostics. In recent years, portable and patient comfortable hand-held optical imagers are developed towards two-dimensional (2D) tumor detections. However, these imagers are not capable of three-dimensional (3D) tomography because they cannot register the positional information of the hand-held probe onto the imaged tissue. A hand-held optical imager has been developed in our Optical Imaging Laboratory with 3D tomography capabilities, as demonstrated from tissue phantom studies. The overall goal of my dissertation is towards the translation of our imager to the clinical setting for 3D tomographic imaging in human breast tissues. A systematic experimental approach was designed and executed as follows: (i) fast 2D imaging, (ii) coregistered imaging, and (iii) 3D tomographic imaging studies. (i) Fast 2D imaging was initially demonstrated in tissue phantoms (1% Liposyn solution) and in vitro (minced chicken breast and 1% Liposyn). A 0.45 cm3 fluorescent target at 1:0 contrast ratio was detectable up to 2.5 cm deep. Fast 2D imaging experiments performed in vivo with healthy female subjects also detected a 0.45 cm3 fluorescent target superficially placed ∼2.5 cm under the breast tissue. (ii) Coregistered imaging was automated and validated in phantoms with ∼0.19 cm error in the probe’s positional information. Coregistration also improved the target depth detection to 3.5 cm, from multi-location imaging approach. Coregistered imaging was further validated in-vivo , although the error in probe’s positional information increased to ∼0.9 cm (subject to soft tissue deformation and movement). (iii) Three-dimensional tomography studies were successfully demonstrated in vitro using 0.45 cm3 fluorescence targets. The feasibility of 3D tomography was demonstrated for the first time in breast tissues using the hand-held optical imager, wherein a 0.45 cm3 fluorescent target (superficially placed) was recovered along with artifacts. Diffuse optical imaging studies were performed in two breast cancer patients with invasive ductal carcinoma. The images showed greater absorption at the tumor cites (as observed from x-ray mammography, ultrasound, and/or MRI). In summary, my dissertation demonstrated the potential of a hand-held optical imager towards 2D breast tumor detection and 3D breast tomography, holding a promise for extensive clinical translational efforts.

Positron emission tomography (PET) tumor segmentation and quantification: Development of new algorithms

Tumor functional volume (FV) and its mean activity concentration (mAC) are the quantities derived from positron emission tomography (PET). These quantities are used for estimating radiation dose for a therapy, evaluating the progression of a disease and also use it as a prognostic indicator for predicting outcome. PET images have low resolution, high noise and affected by partial volume effect (PVE). Manually segmenting each tumor is very cumbersome and very hard to reproduce. To solve the above problem I developed an algorithm, called iterative deconvolution thresholding segmentation (IDTS) algorithm; the algorithm segment the tumor, measures the FV, correct for the PVE and calculates mAC. The algorithm corrects for the PVE without the need to estimate camera's point spread function (PSF); also does not require optimizing for a specific camera. My algorithm was tested in physical phantom studies, where hollow spheres (0.5-16 ml) were used to represent tumors with a homogeneous activity distribution. It was also tested on irregular shaped tumors with a heterogeneous activity profile which were acquired using physical and simulated phantom. The physical phantom studies were performed with different signal to background ratios (SBR) and with different acquisition times (1-5 min). The algorithm was applied on ten clinical data where the results were compared with manual segmentation and fixed percentage thresholding method called T50 and T60 in which 50% and 60% of the maximum intensity respectively is used as threshold. The average error in FV and mAC calculation was 30% and -35% for 0.5 ml tumor. The average error FV and mAC calculation were ~5% for 16 ml tumor. The overall FV error was ∼10% for heterogeneous tumors in physical and simulated phantom data. The FV and mAC error for clinical image compared to manual segmentation was around -17% and 15% respectively. In summary my algorithm has potential to be applied on data acquired from different cameras as its not dependent on knowing the camera's PSF. The algorithm can also improve dose estimation and treatment planning.^

Appendix A. Microfocus X-ray Computed Tomography cross-sectional images of Joergensenium arcticum Ikenoue, Dumitrica and Bjørklund n. sp.

Radiolarians in the Arctic Ocean have been studied lately in both plankton and sediment trap samples in the Chukchi Sea area. These studies have shed light on new radiolarian taxa, especially within the order Entactinaria, including two new species of Joergensenium, Joergensenium arcticum from the western Arctic Ocean, so far restricted to the Pacific Winter Water in the Chukchi Sea, and Joergensenium clevei hitherto found in the northern part of the Norwegian Sea south of the Fram Strait. The taxonomic position of the order Entactinaria is discussed and the genus Joergensenium has been emended. We have also observed in detail the internal structure of J. arcticum using Microfocus X-ray Computed Tomography and have utilized three-dimensional imaging for the first time in a species description.

Analysis of the scale effect in different computed tomography systems on the evaluation of bone tissue parameters

Tra le patologie ossee attualmente riconosciute, l’osteoporosi ricopre il ruolo di protagonista data le sua diffusione globale e la multifattorialità delle cause che ne provocano la comparsa. Essa è caratterizzata da una diminuzione quantitativa della massa ossea e da alterazioni qualitative della micro-architettura del tessuto osseo con conseguente aumento della fragilità di quest’ultimo e relativo rischio di frattura. In campo medico-scientifico l’imaging con raggi X, in particolare quello tomografico, da decenni offre un ottimo supporto per la caratterizzazione ossea; nello specifico la microtomografia, definita attualmente come “gold-standard” data la sua elevata risoluzione spaziale, fornisce preziose indicazioni sulla struttura trabecolare e corticale del tessuto. Tuttavia la micro-CT è applicabile solo in-vitro, per cui l’obiettivo di questo lavoro di tesi è quello di verificare se e in che modo una diversa metodica di imaging, quale la cone-beam CT (applicabile invece in-vivo), possa fornire analoghi risultati, pur essendo caratterizzata da risoluzioni spaziali più basse. L’elaborazione delle immagini tomografiche, finalizzata all’analisi dei più importanti parametri morfostrutturali del tessuto osseo, prevede la segmentazione delle stesse con la definizione di una soglia ad hoc. I risultati ottenuti nel corso della tesi, svolta presso il Laboratorio di Tecnologia Medica dell’Istituto Ortopedico Rizzoli di Bologna, mostrano una buona correlazione tra le due metodiche quando si analizzano campioni definiti “ideali”, poiché caratterizzati da piccole porzioni di tessuto osseo di un solo tipo (trabecolare o corticale), incluso in PMMA, e si utilizza una soglia fissa per la segmentazione delle immagini. Diversamente, in casi “reali” (vertebre umane scansionate in aria) la stessa correlazione non è definita e in particolare è da escludere l’utilizzo di una soglia fissa per la segmentazione delle immagini.