SVM-based texture classification in optical coherence tomography

This paper describes a new method for automated texture classification for glaucoma detection using high resolution retinal Optical Coherence Tomography (OCT). OCT is a non-invasive technique that produces cross-sectional imagery of ocular tissue. Here, we exploit information from OCT im-ages, specifically the inner retinal layer thickness and speckle patterns, to detect glaucoma. The proposed method relies on support vector machines (SVM), while principal component analysis (PCA) is also employed to improve classification performance. Results show that texture features can improve classification accuracy over what is achieved using only layer thickness as existing methods currently do. Index Terms — classification, support vector machine, optical coherence tomography, texture 1

GPU accelerated real-time multi-functional spectral-domain optical coherence tomography system at 1300 nm.

We present a GPU accelerated multi-functional spectral domain optical coherence tomography system at 1300 nm. The system is capable of real-time processing and display of every intensity image, comprised of 512 pixels by 2048 A-lines acquired at 20 frames per second. The update rate for all four images with size of 512 pixels by 2048 A-lines simultaneously (intensity, phase retardation, flow and en face view) is approximately 10 frames per second. Additionally, we report for the first time the characterization of phase retardation and diattenuation by a sample comprised of a stacked set of polarizing film and wave plate. The calculated optic axis orientation, phase retardation and diattenuation match well with expected values. The speed of each facet of the multi-functional OCT CPU-GPU hybrid acquisition system, intensity, phase retardation, and flow, were separately demonstrated by imaging a horseshoe crab lateral compound eye, a non-uniformly heated chicken muscle, and a microfluidic device. A mouse brain with thin skull preparation was imaged in vivo and demonstrated the capability of the system for live multi-functional OCT visualization

Beyond backscattering: Optical neuroimaging by BRAD

Optical coherence tomography (OCT) is a powerful technology for rapid volumetric imaging in biomedicine. The bright field imaging approach of conventional OCT systems is based on the detection of directly backscattered light, thereby waiving the wealth of information contained in the angular scattering distribution. Here we demonstrate that the unique features of few-mode fibers (FMF) enable simultaneous bright and dark field (BRAD) imaging for OCT. As backscattered light is picked up by the different modes of a FMF depending upon the angular scattering pattern, we obtain access to the directional scattering signatures of different tissues by decoupling illumination and detection paths. We exploit the distinct modal propagation properties of the FMF in concert with the long coherence lengths provided by modern wavelength-swept lasers to achieve multiplexing of the different modal responses into a combined OCT tomogram. We demonstrate BRAD sensing for distinguishing differently sized microparticles and showcase the performance of BRAD-OCT imaging with enhanced contrast for ex vivo tumorous tissue in glioblastoma and neuritic plaques in Alzheimer's disease

The Relationship of the Clinical Disc Margin and Bruch's Membrane Opening in Normal and Glaucoma Subjects.

PurposeWe tested the hypotheses that the mismatch between the clinical disc margin (CDM) and Bruch's membrane opening (BMO) is a function of BMO area (BMOA) and is affected by the presence of glaucoma.MethodsA total of 45 normal eyes (45 subjects) and 53 glaucomatous eyes (53 patients) were enrolled and underwent radial optic nerve head (ONH) imaging with spectral domain optical coherence tomography. The inner tip of the Bruch's membrane (BM) and the clinical disc margin were marked on radial scans and optic disc photographs, and were coregistered with custom software. The main outcome measure was the difference between the clinical disc area (CDA) and BMOA, or CDA-BMOA mismatch, as a function of BMOA and diagnosis. Multivariate regression analyses were used to explore the influence of glaucoma and BMOA on the mismatch.ResultsGlobal CDA was larger than BMOA in both groups but the difference was statistically significant only in the normal group (1.98 ± 0.37 vs. 1.85 ± 0.45 mm2, P = 0.02 in the normal group; 1.96 ± 0.38 vs. 1.89 ± 0.56 mm2, P = 0.08 in the glaucoma group). The sectoral CDA-BMOA mismatch was smaller in superotemporal (P = 0.04) and superonasal (P = 0.05) sectors in the glaucoma group. The normalized CDA-BMOA difference decreased with increasing BMOA in both groups (P < 0.001). Presence or severity of glaucoma did not affect the CDA-BMOA difference (P > 0.14).ConclusionsClinical disc area was larger than BMOA in normal and glaucoma eyes but reached statistical significance only in the former group. The CDA-BMOA mismatch diminished with increasing BMOA but was not affected by presence of glaucoma. These findings have important clinical implications regarding clinical evaluation of the ONH

Assessing Retinal Structure In Complete Congenital Stationary Night Blindness and Oguchi Disease

Purpose To examine retinal structure and changes in photoreceptor intensity after dark adaptation in patients with complete congenital stationary night blindness and Oguchi disease. Design Prospective, observational case series. Methods We recruited 3 patients with complete congenital stationary night blindness caused by mutations in GRM6, 2 brothers with Oguchi disease caused by mutations in GRK1, and 1 normal control. Retinal thickness was measured from optical coherence tomography images. Integrity of the rod and cone mosaic was assessed using adaptive optics scanning light ophthalmoscopy. We imaged 5 of the patients after a period of dark adaptation and examined layer reflectivity on optical coherence tomography in a patient with Oguchi disease under light- and dark-adapted conditions. Results Retinal thickness was reduced in the parafoveal region in patients with GRM6 mutations as a result of decreased thickness of the inner retinal layers. All patients had normal photoreceptor density at all locations analyzed. On removal from dark adaptation, the intensity of the rods (but not cones) in the patients with Oguchi disease gradually and significantly increased. In 1 Oguchi disease patient, the outer segment layer contrast on optical coherence tomography was 4-fold higher under dark-adapted versus light-adapted conditions. Conclusions The selective thinning of the inner retinal layers in patients with GRM6 mutations suggests either reduced bipolar or ganglion cell numbers or altered synaptic structure in the inner retina. Our finding that rods, but not cones, change intensity after dark adaptation suggests that fundus changes in Oguchi disease are the result of changes within the rods as opposed to changes at a different retinal locus

Optical coherence tomography- a non-invasive technique applied to conservation of paintings

It is current practice to take tiny samples from a painting to mount and examine in cross-section under a microscope. However, since conservation practice and ethics limit sampling to a minimum and to areas along cracks and edges of paintings, which are often unrepresentative of the whole painting, results from such analyses cannot be taken as representative of a painting as a whole. Recently in a preliminary study, we have demonstrated that near-infrared Optical Coherence Tomography (OCT) can be used directly on paintings to examine the cross-section of paint and varnish layers without contact and the need to take samples. OCT is an optical interferometric technique developed for in vivo imaging of the eye and biological tissues; it is essentially a scanning Michelson’s interferometer with a ‘broadband’ source that has the spatial coherence of a laser. The low temporal coherence and high spatial concentration of the source are the keys to high depth resolution and high sensitivity 3D imaging. The technique is non-invasive and noncontact with a typical working distance of 2 cm. This non-invasive technique enables cross-sections to be examined anywhere on a painting. In this paper, we will report new results on applying near-infrared en-face OCT to paintings conservation and extend the application to the examination of underdrawings, drying processes, and quantitative measurements of optical properties of paint and varnish layers

Directional optical coherence tomography provides accurate outer nuclear layer and Henle fiber layer measurements

Purpose: The outer nuclear layer (ONL) contains photoreceptor nuclei, and its thickness is an important biomarker for retinal degenerations. Accurate ONL thickness measurements are obscured in standard optical coherence tomography (OCT) images because of Henle fiber layer (HFL). Improved differentiation of the ONL and HFL boundary is made possible by using directional OCT, a method that purposefully varies the pupil entrance position of the OCT beam. Methods: Fifty-seven normal eyes were imaged using multiple pupil entry positions with a commercial spectral domain OCT system. Cross-sectional image sets were registered to each other and segmented at the top of HFL, the border of HFL and the ONL and at the external limiting membrane. Thicknesses of the ONL and HFL were measured and analyzed. Results: The true ONL and HFL thicknesses varied substantially by eccentricity and between individuals. The true macular ONL thickness comprised an average of 54.6% of measurements that also included HFL. The ONL and HFL thicknesses at specific retinal eccentricities were poorly correlated. Conclusion: Accurate ONL and HFL thickness measurements are made possible by the optical contrast of directional OCT. Distinguishing these individual layers can improve clinical trial endpoints and assessment of disease progression

Developing non-destructive techniques to predict 'Hayward' kiwifruit storability : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Food Technology at Massey University, Palmerston North, New Zealand

A significant portion of New Zealand’s kiwifruit production is held as stock in local coolstores for extended periods of time before being exported. Many pre-harvest factors contribute to variation in fruit quality at harvest and during coolstorage, and results in the difficulty in segregating fruit for their storage outcomes. The objective of this work was to develop non-destructive techniques utilised at harvest to predict storability of individual or batches of ‘Hayward’ kiwifruit based on (near) skin properties. Segregation of fruit with low storage potential at harvest could enable that fruit to be sold earlier in the season reducing total fruit loss and improving profitability later in the season. The potential for optical coherence tomography (OCT) to detect near surface cellular structural differences in kiwifruit as a result of preharvest factors was demonstrated through quantitative image analysis of 3D OCT images of intact fruit from five commercial cultivars. Visualisation and characterisation of large parenchyma cells in the outer pericarp of kiwifruit was achieved by developing an automated image processing technique. This work established the usefulness of OCT to perform rapid analysis and differentiation of the microstructures of sub-surface cells between kiwifruit cultivars. However, the effects of preharvest conditions between batches of fruit within a cultivar were not detectable from image analysis and hence, the ability to provide segregation or prediction for fruit from the same cultivar was assumed to be limited. Total soluble solids concentration (TSS) and flesh firmness (FF) are two important quality attributes indicating the eating quality and storability of stored kiwifruit. Prediction of TSS and FF using non-destructive techniques would allow strategic marketing of fruit. This work demonstrated that visible-near-infrared (Vis-NIR) spectroscopy could be utilised as the sole input at harvest, to provide quantitative prediction of post-storage TSS by generating blackbox regression models. However the level of accuracy achieved was not adequate for online sorting purposes. Quantitative prediction of FF remained unsuccessful. Improved ways of physical measurements for FF may help reduce the undesirable variation observed on the same fruit and increase prediction capability. More promising results were obtained by developing blackbox classification models using Vis-NIR spectroscopy at harvest to segregate storability of individual kiwifruit based on the export FF criterion of 1 kgf (9.8 N). Through appropriate machine learning techniques, the surface properties of fruit at harvest captured in the form of spectral data were correlated to post-storage FF via pattern recognition. The best prediction was obtained for fruit stored at 0°C for 125 days: approximately 50% of the soft fruit and 80% of the good fruit could be identified. The developed model was capable of performing classification both within (at the fruit level) and between grower lines. Model validation suggested that segregation between grower lines at harvest achieved 30% reduction in soft fruit after storage. Should the model be applied in the industry to enable sequential marketing, $11.2 million NZD/annum could be saved because of reduced fruit loss, repacking and condition checking costs