Processing and rendering of Fourier domain optical coherence tomography images at a line rate over 524 kHz using a graphics processing unit

In Fourier domain optical coherence tomography (FD-OCT), a large amount of interference data needs to be resampled from the wavelength domain to the wavenumber domain prior to Fourier transformation. We present an approach to optimize this data processing, using a graphics processing unit (GPU) and parallel processing algorithms. We demonstrate an increased processing and rendering rate over that previously reported by using GPU paged memory to render data in the GPU rather than copying back to the CPU. This avoids unnecessary and slow data transfer, enabling a processing and display rate of well over 524,000 A-scan/s for a single frame. To the best of our knowledge this is the fastest processing demonstrated to date and the first time that FD-OCT processing and rendering has been demonstrated entirely on a GPU.

Effect of Disease Severity and Optic Disc Size on Diagnostic Accuracy of RTVue Spectral Domain Optical Coherence Tomograph in Glaucoma

PURPOSE. To evaluate the effect of disease severity and optic disc size on the diagnostic accuracies of optic nerve head (ONH), retinal nerve fiber layer (RNFL), and macular parameters with RTVue (Optovue, Fremont, CA) spectral domain optical coherence tomography (SDOCT) in glaucoma. METHODS. 110 eyes of 62 normal subjects and 193 eyes of 136 glaucoma patients from the Diagnostic Innovations in Glaucoma Study underwent ONH, RNFL, and macular imaging with RTVue. Severity of glaucoma was based on visual field index (VFI) values from standard automated perimetry. Optic disc size was based on disc area measurement using the Heidelberg Retina Tomograph II (Heidelberg Engineering, Dossenheim, Germany). Influence of disease severity and disc size on the diagnostic accuracy of RTVue was evaluated by receiver operating characteristic (ROC) and logistic regression models. RESULTS. Areas under ROC curve (AUC) of all scanning areas increased (P < 0.05) as disease severity increased. For a VFI value of 99%, indicating early damage, AUCs for rim area, average RNLI thickness, and ganglion cell complex-root mean square were 0.693, 0.799, and 0.779, respectively. For a VFI of 70%, indicating severe damage, corresponding AUCs were 0.828, 0.985, and 0.992, respectively. Optic disc size did not influence the AUCs of any of the SDOCT scanning protocols of RTVue (P > 0.05). Sensitivity of the rim area increased and specificity decreased in large optic discs. CONCLUSIONS. Diagnostic accuracies of RTVue scanning protocols for glaucoma were significantly influenced by disease severity. Sensitivity of the rim area increased in large optic discs at the expense of specificity. (Invest Ophthalmol Vis Sci. 2011;92:1290-1296) DOI:10.1167/iovs.10-5516

Comparison of Different Spectral Domain Optical Coherence Tomography Scanning Areas for Glaucoma Diagnosis

Purpose: To evaluate retinal nerve fiber layer (RNFL), optic nerve head (ONH), and macular thickness measurements for glaucoma detection using the RTVue spectral domain optical coherence tomograph. Design: Diagnostic, case-control study. Participants: One hundred forty eyes of 106 glaucoma patients and 74 eyes of 40 healthy subjects from the Diagnostic Innovations in Glaucoma Study (DIGS). Methods: All patients underwent ocular imaging with the commercially available RTVue. Optic nerve head, RNFL thickness, and macular thickness scans were obtained during the same visit. Receiver operating characteristic (ROC) curves and sensitivities at fixed specificities (80% and 95%) were calculated for each parameter. Main Outcome Measures: Areas under the ROC curves (AUC) and sensitivities at fixed specificities of 80% and 95%. Results: The AUC for the RNFL parameter with best performance, inferior quadrant thickness, was significantly higher than that of the best-performing ONH parameter, inferior rim area (0.884 vs 0.812, respectively; P = 0.04). There was no difference between ROC curve areas of the best RNFL thickness parameters and the best inner macular thickness measurement, ganglion cell complex root mean square (ROC curve area = 0.870). Conclusions: The RTVue RNFL and inner retinal macular thickness measurements had good ability to detect eyes with glaucomatous visual field loss and performed significantly better than ONH parameters.

Nonlinear filtering in object and Fourier space in a joint transform optical correlator: comparison and experimental realization

The use of different kinds of nonlinear filtering in a joint transform correlator are studied and compared. The study is divided into two parts, one corresponding to object space and the second to the Fourier domain of the joint power spectrum. In the first part, phase and inverse filters are computed; their inverse Fourier transforms are also computed, thereby becoming the reference in the object space. In the Fourier space, the binarization of the power spectrum is realized and compared with a new procedure for removing the spatial envelope. All cases are simulated and experimentally implemented by a compact joint transform correlator.

Mean sea surface modelling from multi-satellite altimetry utilising frequency domain techniques

A technique is presented for the development of a high precision and resolution Mean Sea Surface (MSS) model. The model utilises Radar altimetric sea surface heights extracted from the geodetic phase of the ESA ERS-1 mission. The methodology uses a modified Le Traon et al. (1995) cubic-spline fit of dual ERS-1 and TOPEX/Poseidon crossovers for the minimisation of radial orbit error. The procedure then uses Fourier domain processing techniques for spectral optimal interpolation of the mean sea surface in order to reduce residual errors within the model. Additionally, a multi-satellite mean sea surface integration technique is investigated to supplement the first model with additional enhanced data from the GEOSAT geodetic mission.The methodology employs a novel technique that combines the Stokes' and Vening-Meinsz' transformations, again in the spectral domain. This allows the presentation of a new enhanced GEOSAT gravity anomaly field.

Fractional dynamics of genetic algorithms using hexagonal space tessellation

The paper formulates a genetic algorithm that evolves two types of objects in a plane. The fitness function promotes a relationship between the objects that is optimal when some kind of interface between them occurs. Furthermore, the algorithm adopts an hexagonal tessellation of the two-dimensional space for promoting an efficient method of the neighbour modelling. The genetic algorithm produces special patterns with resemblances to those revealed in percolation phenomena or in the symbiosis found in lichens. Besides the analysis of the spacial layout, a modelling of the time evolution is performed by adopting a distance measure and the modelling in the Fourier domain in the perspective of fractional calculus. The results reveal a consistent, and easy to interpret, set of model parameters for distinct operating conditions.

Fractional Dynamics in the Rayleigh's Piston

This paper studies the dynamics of the Rayleigh piston using the modeling tools of Fractional Calculus. Several numerical experiments examine the effect of distinct values of the parameters. The time responses are transformed into the Fourier domain and approximated by means of power law approximations. The description reveals characteristics usual in Fractional Brownian phenomena.

Coifman-aallokkeet ja skaalaussuotimen muodostus differentiaalievoluut ion avulla

Ortogonaalisen M-kaistaisen moniresoluutioanalyysin matemaattiset perusteet esitetään yksityiskohtaisesti. Coifman-aallokkeiden määritelmä yleistetään dilaatiokertoimelle M ja nollasta poikkeavalle häviävien momenttien keskukselle.Funktion approksimointia näytepisteistä aallokkeiden avulla pohditaan ja erityisesti esitetään approksimaation asymptoottinen virhearvio Coifman-aallokkeille. Skaalaussuotimelle osoitetaan välttämättömät ja riittävät ehdot, jotka johtavat yleistettyihin Coifman-aallokkeisiin. Moniresoluutioanalyysin tiheys todistetaansuoraan Lebesguen integraalin määritelmään perustuen yksikön partitio-ominaisuutta käyttäen. Todistus on riittävä sellaisenaan avaruudessa L2(Wd) käyttämättä Fourier-tason ominaisuuksia tai ehtoja. Mallatin algoritmi johdetaan M-kaistaisille aallokkeille ja moniuloitteisille signaaleille. Algoritmille esitetään myös rekursiivinen muoto. Differentiaalievoluutioalgoritmin avulla ratkaistaan Coifman-aallokkeisiin liittyvien skaalaussuotimien kertoimien arvoja useille skaalausfunktiolle. Approksimaatio- ja kuvanpakkausesimerkkejä esitetään menetelmien havainnollistamiseksi. Differentiaalievoluutioalgoritmin avulla etsitään myös referenssikuville optimoitu skaalaussuodin. Löydetty suodin on regulaarinen ja erittäinsymmetrinen.

Imagerie à haut contraste et caractérisation d'exoplanètes par la spectroscopie intégrale de champ

Cette thèse porte sur l’amélioration des techniques d’imagerie à haut-contraste permettant la détection directe de compagnons à de faibles séparations de leur étoile hôte. Plus précisément, elle s’inscrit dans le développement du Gemini Planet Imager (GPI) qui est un instrument de deuxième génération pour les télescopes Gemini. Cette caméra utilisera un spectromètre à champ intégral (SCI) pour caractériser les compagnons détectés et pour réduire le bruit de tavelure limitant leur détection et corrigera la turbulence atmosphérique à un niveau encore jamais atteint en utilisant deux miroirs déformables dans son système d’optique adaptative (OA) : le woofer et le tweeter. Le woofer corrigera les aberrations de basses fréquences spatiales et de grandes amplitudes alors que le tweeter compensera les aberrations de plus hautes fréquences ayant une plus faible amplitude. Dans un premier temps, les performances pouvant être atteintes à l’aide des SCIs présentement en fonction sur les télescopes de 8-10 m sont investiguées en observant le compagnon de l’étoile GQ Lup à l’aide du SCI NIFS et du système OA ALTAIR installés sur le télescope Gemini Nord. La technique de l’imagerie différentielle angulaire (IDA) est utilisée pour atténuer le bruit de tavelure d’un facteur 2 à 6. Les spectres obtenus en bandes JHK ont été utilisés pour contraindre la masse du compagnon par comparaison avec les prédictions des modèles atmosphériques et évolutifs à 8−60 MJup, où MJup représente la masse de Jupiter. Ainsi, il est déterminé qu’il s’agit plus probablement d’une naine brune que d’une planète. Comme les SCIs présentement en fonction sont des caméras polyvalentes pouvant être utilisées pour plusieurs domaines de l’astrophysique, leur conception n’a pas été optimisée pour l’imagerie à haut-contraste. Ainsi, la deuxième étape de cette thèse a consisté à concevoir et tester en laboratoire un prototype de SCI optimisé pour cette tâche. Quatre algorithmes de suppression du bruit de tavelure ont été testés sur les données obtenues : la simple différence, la double différence, la déconvolution spectrale ainsi qu’un nouvel algorithme développé au sein de cette thèse baptisé l’algorithme des spectres jumeaux. Nous trouvons que l’algorithme des spectres jumeaux est le plus performant pour les deux types de compagnons testés : les compagnons méthaniques et non-méthaniques. Le rapport signal-sur-bruit de la détection a été amélioré d’un facteur allant jusqu’à 14 pour un compagnon méthanique et d’un facteur 2 pour un compagnon non-méthanique. Dernièrement, nous nous intéressons à certains problèmes liés à la séparation de la commande entre deux miroirs déformables dans le système OA de GPI. Nous présentons tout d’abord une méthode utilisant des calculs analytiques et des simulations Monte Carlo pour déterminer les paramètres clés du woofer tels que son diamètre, son nombre d’éléments actifs et leur course qui ont ensuite eu des répercussions sur le design général de l’instrument. Ensuite, le système étudié utilisant un reconstructeur de Fourier, nous proposons de séparer la commande entre les deux miroirs dans l’espace de Fourier et de limiter les modes transférés au woofer à ceux qu’il peut précisément reproduire. Dans le contexte de GPI, ceci permet de remplacer deux matrices de 1600×69 éléments nécessaires pour une séparation “classique” de la commande par une seule de 45×69 composantes et ainsi d’utiliser un processeur prêt à être utilisé plutôt qu’une architecture informatique plus complexe.

Hiperautofluorescencia foveal como factor predictor de recuperación visual en pacientes con desprendimiento regmatógeno de retina

Introducción: una de las causas de pobre ganancia visual luego de un tratamiento exitoso de desprendimiento de retina, sin complicaciones, es el daño de los fotoreceptores, reflejada en una disrupción de la capa de la zona elipsoide y membrana limitante externa (MLE). En otras patologías se ha demostrado que la hiperautofluorescencia foveal se correlaciona con la integridad de la zona elipsoide y MLE y una mejor recuperación visual. Objetivos: evaluar la asociación entre la hiperautofluorescencia foveal, la integridad de la capa de la zona elipsoide y recuperación visual luego de desprendimiento de retina regmatógeno (DRR) exitosamente tratado. Evaluar la concordancia inter-evaluador de estos exámenes. Metodología: estudio de corte transversal de autofluorescencia foveal y tomografía óptica coherente macular de dominio espectral en 65 pacientes con DRR evaluados por 3 evaluadores independientes. La concordancia inter-evaluador se estudio mediante Kappa de Cohen y la asociación entre las diferentes variables mediante la prueba chi cuadrado y pruebas Z para comparación de proporciones. Resultados: La concordancia de la autofluorescencia fue razonable y la de la tomografía óptica coherente macular buena a muy buena. Sujetos que presentaron hiperautofluorescencia foveal asociada a integridad de la capa de la zona elipsoide tuvieron 20% más de posibilidad de recuperar agudeza visual final mejor a 20/50 que los que no cumplieron éstas características. Conclusión: Existe una asociación clínicamente importante entre la hiperautofluorescencia foveal, la integridad de la capa de zona elipsoide y la mejor agudeza visual final, sin embargo ésta no fue estadísticamente significativa (p=0.39)

Factores asociados a recuperación visual deficiente después de cirugía exitosa para desprendimiento de retina regmatógeno

Introducción: Varias características pueden afectar el pronóstico visual después de resolver quirúrgicamente el desprendimiento de retina. Existen características no observables por el ojo humano por si solo pero si por tomografía óptica coherente que se relacionan con la recuperación visual. Objetivo: Describir las características clínicas y topográfica en los periodos pre y postquirúrgico de ojos que ha sufrido DR regmatógeno con compromiso macular y su relación con la calidad de recuperación visual después de una cirugía considerada exitosa desde el punto de vista anatómico. Materiales y métodos: Estudio descriptivo en el que se comparan algunas características en tres periodos perioeperatorios, uno antes y dos después de cirugía (3 y 6 meses) de 24 ojos con DRregmatógeno y compromiso macular intervenidos mediante retinopexia combinada con vitrectomía pars plana. Resultados: La recuperación visual mejor o igual que logMAR 0,397 (20/50) se dió en 41,7% de ojos y 16,7%. alcanzaron agudeza visual logMAR 0,301 (20/40). Cinco ojos no alcanzaron una ganancia de líneas de visión mayor a cinco. El líquido submacular ausente se observó en la mayoría de ojos que recuperaron más de cinco líneas al igual que aquellos con elipsoide conservado. La regularidad del neuroepitelio y el edema en el periodo posquirúrgico no mostraron comportamientos claros respecto a recuperación visual al igual que la altura del desprendimiento y el número de cuadrantes afectados. Una mejor recuperación visual fue más frecuente en aquellos con menos de cinco semanas de desprendimiento de retina. Conclusiones: El retraso menor a cinco semanas en la resolución del desprendimiento de retina, la conservación del elipsoide y la ausencia de líquido submacular en el periodo postquirúrgico se observó más frecuentemente en ojos con mejor recuperación visual.

Retinal nerve fiber evaluation in neuro-ophthalmic diseases of the anterior visual pathway

Retinal nerve fiber evaluation is important in the diagnosis and management of several diseases of the anterior visual pathway. In this report we review the clinical findings and the current techonologies avalilable to analyse the retinal nerve fiber layer. We furthermore review the main findings in several disease of the anterior visual pathways including inflammatory, ischemic, toxics, hereditary, compressive and traumatic optic neuropathies as well as lesion of the optic chiasm, optic tract and lateral geniculate body.

Locating the source of volcanic tremor at stromboli volcano, italy

We have developed a method for locating sources of volcanic tremor and applied it to a dataset recorded on Stromboli volcano before and after the onset of the February 27th 2007 effusive eruption. Volcanic tremor has attracted considerable attention by seismologists because of its potential value as a tool for forecasting eruptions and for better understanding the physical processes that occur inside active volcanoes. Commonly used methods to locate volcanic tremor sources are: 1) array techniques, 2) semblance based methods, 3) calculation of wave field amplitude. We have choosen the third approach, using a quantitative modeling of the seismic wavefield. For this purpose, we have calculated the Green Functions (GF) in the frequency domain with the Finite Element Method (FEM). We have used this method because it is well suited to solve elliptic problems, as the elastodynamics in the Fourier domain. The volcanic tremor source is located by determining the source function over a regular grid of points. The best fit point is choosen as the tremor source location. The source inversion is performed in the frequency domain, using only the wavefield amplitudes. We illustrate the method and its validation over a synthetic dataset. We show some preliminary results on the Stromboli dataset, evidencing temporal variations of the volcanic tremor sources.

Repeatability and reproducibility of corneal thickness using SOCT Copernicus HR

Purpose: The aim of this study is to determine the reliability of corneal thickness measurements derived from SOCT Copernicus HR (Fourier domain OCT). Methods: Thirty healthy eyes of 30 subjects were evaluated. One eye of each patient was chosen randomly. Images were obtained of the central (up to 2.0 mm from the corneal apex) and paracentral (2.0 to 4.0 mm) cornea. We assessed corneal thickness (central and paracentral) and epithelium thickness. The intra-observer repeatability data were analysed using the intra-class correlation coefficient (ICC) for a range of 95 per cent within-subject standard deviation (SW) and the within-subject coefficient of variation (CW). The level of agreement by Bland–Altman analysis was also represented for the study of the reproducibility between observers and agreement between methods of measurement (automatic versus manual). Results: The mean value of the central corneal thickness (CCT) was 542.4 ± 30.1 μm (SD). There was a high intra-observer agreement, finding the best result in the central sector with an intra-class correlation coefficient of 0.99, 95 per cent CI (0.989 to 0.997) and the worst, in the minimum corneal thickness, with an intra-class correlation coefficient of 0.672, 95 per cent CI (0.417 to 0.829). Reproducibility between observers was very high. The best result was found in the central sector thickness obtained both manually and automatically with an intra-class correlation coefficient of 0.990 in both cases and the worst result in the maximum corneal thickness with an intra-class correlation coefficient of 0.827. The agreement between measurement methods was also very high with intra-class correlation coefficient greater than 0.91. On the other hand the repeatability and reproducibility for epithelial measurements was poor. Conclusion: Pachymetric mapping with SOCT Copernicus HR was found to be highly repeatable and reproducible. We found that the device lacks an appropriate ergonomic design as proper focusing of the laser beam onto the cornea for anterior segment scanning required that patients were positioned slightly farther away from the machine head-rest than in the setup for retinal imaging.

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.