Retinal boundary segmentation in stargardt disease optical coherence tomography images using automated deep learning

Purpose: To use a deep learning model to develop a fully automated method (fully semantic network and graph search [FS-GS]) of retinal segmentation for optical coherence tomography (OCT) images from patients with Stargardt disease. Methods: Eighty-seven manually segmented (ground truth) OCT volume scan sets (5171 B-scans) from 22 patients with Stargardt disease were used for training, validation and testing of a novel retinal boundary detection approach (FS-GS) that combines a fully semantic deep learning segmentation method, which generates a per-pixel class prediction map with a graph-search method to extract retinal boundary positions. The performance was evaluated using the mean absolute boundary error and the differences in two clinical metrics (retinal thickness and volume) compared with the ground truth. The performance of a separate deep learning method and two publicly available software algorithms were also evaluated against the ground truth. Results: FS-GS showed an excellent agreement with the ground truth, with a boundary mean absolute error of 0.23 and 1.12 pixels for the internal limiting membrane and the base of retinal pigment epithelium or Bruch's membrane, respectively. The mean difference in thickness and volume across the central 6 mm zone were 2.10 µm and 0.059 mm3. The performance of the proposed method was more accurate and consistent than the publicly available OCTExplorer and AURA tools. Conclusions: The FS-GS method delivers good performance in segmentation of OCT images of pathologic retina in Stargardt disease. Translational Relevance: Deep learning models can provide a robust method for retinal segmentation and support a high-throughput analysis pipeline for measuring retinal thickness and volume in Stargardt disease

The effect of transverse ocular magnification adjustment on macular thickness profile in different refractive errors in community-based adults

Purpose Changes in retinal thickness are common in various ocular diseases. Transverse magnification due to differing ocular biometrics, in particular axial length, affects measurement of retinal thickness in different regions. This study evaluated the effect of axial length and refractive error on measured macular thickness in two community-based cohorts of healthy young adults. Methods A total of 2160 eyes of 1247 community-based participants (18–30 years; 23.4% myopes, mean axial length = 23.6mm) were included in this analysis. Macular thickness measurements were obtained using a spectral-domain optical coherence tomography (which assumes an axial length of 24.385mm). Using a custom program, retinal thickness data were extracted at the 9 Early Treatment of Diabetic Retinopathy Study (ETDRS) regions with and without correction for transverse magnificent effects, with the corrected measurements adjusting according to the participant’s axial length. Linear mixed models were used to analyse the effect of correction and its interaction with axial length or refractive group on retinal thickness. Results The raw measures (uncorrected for axial length) underestimated the true retinal thickness at the central macula, while overestimating at most non-central macular regions. There was an axial length by correction interaction effect in all but the nasal regions (all p\u3c0.05). For each 1mm increase in axial length, the central macular thickness is overestimated by 2.7–2.9μm while thicknesses at other regions were underestimated by 0.2–4.1μm. Based on the raw thickness measurements, myopes have thinner retinas than non-myopes at most non-central macular. However, this difference was no longer significant when the corrected data was used. Conclusion In a community-based sample, the raw measurements underestimate the retinal thickness at the central macula and overestimate the retinal thickness at non-central regions of the ETDRS grid. The effect of axial length and refractive error on retinal thickness is reduced after correcting for transverse magnification effects resulting from axial length differences

Influence of the time of day on axial length and choroidal thickness changes to hyperopic and myopic defocus in human eyes

© 2019 Elsevier Ltd. This manuscript version is made available under the CC-BY-NC-ND 4.0 license: http://creativecommons.org/licenses/by-nc-nd/4.0/ This author accepted manuscript is made available following 12 month embargo from date of publication (March 2019) in accordance with the publisher’s archiving policyResearch in animal models have shown that exposing the eye to positive or negative spectacle lenses can lead to predictable changes in eye growth. Recent research indicates that brief periods (1–2 h) of monocular defocus results in small, but significant changes in axial length and choroidal thickness of human subjects. However, the effects of the time of day on these ocular changes with defocus are not known. In this study, we examined the effects of monocular myopic and hyperopic defocus on axial length and choroidal thickness when applied in the morning (change between 10 a.m. and 12 p.m.) vs the evening (change between 5 and 7 p.m.) in young adult human participants (mean age, 23.44 ± 4.52 years). A series of axial length (using an IOL Master) and choroidal thickness (using an optical coherence tomographer) measurements were obtained over three consecutive days in both eyes. Day 1 (no defocus) examined the baseline ocular measurements in the morning (10 a.m. and 12 p.m.) and in the evening (5 and 7 p.m.), day 2 investigated the effects of hyperopic and myopic defocus on ocular parameters in the morning (subjects wore a spectacle lens with +3 or −3 DS over the right eye and a plano lens over the left eye between 10 a.m. and 12 p.m.), and day 3 examined the effects of defocus in the evening (+3 or −3 DS spectacle lens over the right eye between 5 and 7 p.m.). Exposure to myopic defocus caused a significant reduction in axial length and thickening of the subfoveal choroid at both times; but, compared to baseline data from day 1, the relative change in axial length (−0.021 ± 0.009 vs +0.004 ± 0.003 mm, p = 0.009) and choroidal thickness (+0.027 ± 0.006 vs +0.007 ± 0.006 mm, p = 0.011) with defocus were significantly greater for evening exposure to defocus than for the morning session. On the contrary, introduction of hyperopic defocus resulted in a significant increase in axial length when given in the morning (+0.026 ± 0.006 mm), but not in the evening (+0.001 ± 0.003 mm) (p = 0.047). Furthermore, hyperopic defocus resulted in a significant thinning of the choroid (p = 0.005), but there was no significant influence of the time of day on choroidal changes associated with hyperopic defocus (p = 0.672). Exposure to hyperopic and myopic defocus at different times of the day was also associated with changes in the parafoveal regions of the choroid (measured across 1.5 mm nasal and temporal choroidal regions on either side of the fovea). Our results show that ocular response to optical defocus varies significantly depending on the time of day in human subjects. These findings represent a potential interaction between the signal associated with the eye's natural diurnal rhythm and the visual signal associated with the optical defocus, making the eye perhaps more responsive to hyperopic defocus (or ‘go’ signal) in the morning, and to myopic defocus (or ‘stop’ signal) in the latter half of the day

Energy-dispersive X-ray absorption spectroscopy at LNLS: Investigation on strongly correlated metal oxides

An energy-dispersive X-ray absorption spectroscopy beamline mainly dedicated to X-ray magnetic circular dichroism (XMCD) and material science under extreme conditions has been implemented in a bending-magnet port at the Brazilian Synchrotron Light Laboratory. Here the beamline technical characteristics are described, including the most important aspects of the mechanics, optical elements and detection set-up. The beamline performance is then illustrated through two case studies on strongly correlated transition metal oxides: an XMCD insight into the modifications of the magnetic properties of Cr-doped manganites and the structural deformation in nickel perovskites under high applied pressure. © 2010 International Union of Crystallography. Printed in Singapore - all rights reserved.Fil: Cezar, Julio C.. Laboratorio Nacional de Luz Síncrotron; BrasilFil: Souza Neto, Narcizo M.. Laboratorio Nacional de Luz Síncrotron; BrasilFil: Piamonteze, Cínthia. Laboratorio Nacional de Luz Síncrotron; BrasilFil: Tamura, Edilson. Laboratorio Nacional de Luz Síncrotron; BrasilFil: Garcia, Flávio. Laboratorio Nacional de Luz Síncrotron; BrasilFil: Carvalho, Edson J.. Laboratorio Nacional de Luz Síncrotron; BrasilFil: Neueschwander, Régis T.. Laboratorio Nacional de Luz Síncrotron; BrasilFil: Ramos, Aline Y.. Centre National de la Recherche Scientifique; FranciaFil: Tolentino, Hélio C. N.. Centre National de la Recherche Scientifique; FranciaFil: Caneiro, Alberto. Comisión Nacional de Energía Atómica. Centro Atómico Bariloche; Argentina. Comisión Nacional de Energía Atómica. Gerencia del Área de Energía Nuclear. Instituto Balseiro; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Massa, Nestor Emilio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Química Inorgánica "Dr. Pedro J. Aymonino". Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Química Inorgánica "Dr. Pedro J. Aymonino"; ArgentinaFil: Martinez Lope, Maria Jesus. Instituto de Ciencia de Materiales de Madrid; España. Consejo Superior de Investigaciones Científicas; EspañaFil: Alonso, José Antonio. Instituto de Ciencia de Materiales de Madrid; España. Consejo Superior de Investigaciones Científicas; EspañaFil: Itié, Jean Paul. L'Orme des Merisiers. Synchrotron SOLEIL; Franci

Dynamic OCT measurement of corneal deformation by an air puff in normal and cross-linked corneas

A new technique is presented for the non-invasive imaging of the dynamic response of the cornea to an air puff inducing a deformation. A spectral OCT instrument combined with an air tonometer in a non-collinear configuration was used to image the corneal deformation over full corneal cross-sections, as well as to obtain high speed measurements of the temporal evolution of the corneal apex. The entire deformation process can be dynamically visualized. A quantitative analysis allows direct extraction of several deformation parameters, such as amplitude, diameter and volume of the maximum deformation, as well as duration and speed of the increasing deformation period and the recovery period. The potential of the technique is demonstrated on porcine corneas in vitro under constant IOP for several conditions (untreated, after riboflavin instillation and under cross-linking with ultraviolet light), as well as on human corneas in vivo. The new technique has proved very sensitive to detect differences in the deformation parameters across conditions. We have confirmed non-invasively that Riboflavin and UV-cross-linking induce changes in the corneal biomechanical properties. Those differences appear to be the result of changes in constituent properties of the cornea, and not a consequence of changes in corneal thickness, geometry or IOP. These measurements are a first step for the estimation of the biomechanical properties of corneal tissue, at an individual level and in vivo, to improve diagnosis and prognosis of diseases and treatments involving changes in the biomechanical properties of the cornea

Revisiting the Crystal Structure of BaCe0.4Zr0.4Y0.2O3-δ Proton Conducting Perovskite and Its Correlation with Transport Properties

Oxides with proton conductivity have a great potential for applications in environmental energy technology. Despite the BaCe0.4Zr0.4Y0.2O3-δ (BCZY) perovskites being well-known proton conductors, it is a challenge to determine the optimal operating temperature range where the energy applications benefit most from this unique property. The protonic transport properties strongly depend on crystal structure and local distortions in the participating cation coordination sphere, according to related temperatures and gas feed. The transport and crystallographic properties of BCZY were simultaneously studied by impedance spectroscopy (IS) and synchrotron X-ray diffraction (S-XRD). A strong correlation between conductivity and the lattice parameter, corresponding in principle to a cubic symmetry, was observed, mainly between 400 and 700 °C. The protonic conductivity range was analyzed by the H/D isotopic effect on the impedance spectra, which helped to identify protonic conduction as the governing transport mechanism below 600 °C, while the transport via oxygen vacancies dominates above this temperature. In order to assess the real crystallographic structure, the simultaneous refinement of laboratory XRD and neutron diffraction (ND) patterns was performed. According to this, BCZY changes from rhombohedral symmetry below 400 °C to cubic at 600 °C in a second-order phase transition. Complementary quasielastic neutron scattering (QENS) enables us to determine a protonic jump length of 3.1 Å, which matches the O-O distances in the octahedral oxygen coordination sphere around the cations. These results support the protonic self-diffusion through proton hopping between intraoctahedral O sites as the main transport mechanism up to 600 °C.Fil: Basbus, Juan Felipe. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología - Nodo Bariloche | Comisión Nacional de Energía Atómica. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología - Nodo Bariloche; ArgentinaFil: Arce, Mauricio Damián. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología - Nodo Bariloche | Comisión Nacional de Energía Atómica. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología - Nodo Bariloche; ArgentinaFil: Napolitano, Federico Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología - Nodo Bariloche | Comisión Nacional de Energía Atómica. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología - Nodo Bariloche; ArgentinaFil: Troiani, Horacio Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología - Nodo Bariloche | Comisión Nacional de Energía Atómica. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología - Nodo Bariloche; ArgentinaFil: Alonso, José Antonio. Instituto de Ciencia de Materiales de Madrid; EspañaFil: Saleta, Martin Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología - Nodo Bariloche | Comisión Nacional de Energía Atómica. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología - Nodo Bariloche; Argentina. Centro Nacional de Pesquisa em Energia e Materiais; BrasilFil: González, Miguel A.. Institut Laue Langevin; FranciaFil: Cuello, Gabriel Julio. Institut Laue Langevin; FranciaFil: Fernández Díaz, María Teresa. Institut Laue Langevin; FranciaFil: Pardo Sainz, Miguel. Universidad de Zaragoza. Instituto de Ciencias de Materiales de Aragon; EspañaFil: Bonanos, Nikolaos. Technical University of Denmark; DinamarcaFil: Jimenez, Catalina Elena. Helmholtz-Zentrum; AlemaniaFil: Giebeler, Lars. No especifíca;Fil: Figueroa, Santiago J. A.. Centro Nacional de Pesquisa em Energia e Materiais; BrasilFil: Caneiro, Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología - Nodo Bariloche | Comisión Nacional de Energía Atómica. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología - Nodo Bariloche; ArgentinaFil: Serquis, Adriana Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología - Nodo Bariloche | Comisión Nacional de Energía Atómica. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología - Nodo Bariloche; ArgentinaFil: Mogni, Liliana Verónica. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología - Nodo Bariloche | Comisión Nacional de Energía Atómica. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología. Unidad Ejecutora Instituto de Nanociencia y Nanotecnología - Nodo Bariloche; Argentin

Optical coherence tomography-based contact indentation for diaphragm mechanics in a mouse model of transforming growth factor alpha induced lung disease

This study tested the utility of optical coherence tomography (OCT)-based indentation to assess mechanical properties of respiratory tissues in disease. Using OCT-based indentation, the elastic modulus of mouse diaphragm was measured from changes in diaphragm thickness in response to an applied force provided by an indenter. We used a transgenic mouse model of chronic lung disease induced by the overexpression of transforming growth factor-alpha (TGF-a), established by the presence of pleural and peribronchial fibrosis and impaired lung mechanics determined by the forced oscillation technique and plethysmography. Diaphragm elastic modulus assessed by OCT-based indentation was reduced by TGF-a at both left and right lateral locations (p < 0.05). Diaphragm elastic modulus at left and right lateral locations were correlated within mice (r = 0.67, p < 0.01) suggesting that measurements were representative of tissue beyond the indenter field. Co-localised images of diaphragm after TGF-a overexpression revealed a layered fibrotic appearance. Maximum diaphragm force in conventional organ bath studies was also reduced by TGF-a overexpression (p < 0.01). Results show that OCT-based indentation provided clear delineation of diseased diaphragm, and together with organ bath assessment, provides new evidence suggesting that TGF-a overexpression produces impairment in diaphragm function and, therefore, an increase in the work of breathing in chronic lung disease

Energy-dispersive X-ray absorption spectroscopy at LNLS: investigation on strongly correlated metal oxides

An energy-dispersive X-ray absorption spectroscopy beamline mainly dedicated to X-ray magnetic circular dichroism (XMCD) and material science under extreme conditions has been implemented in a bending-magnet port at the Brazilian Synchrotron Light Laboratory. Here the beamline technical characteristics are described, including the most important aspects of the mechanics, optical elements and detection set-up. The beamline performance is then illustrated through two case studies on strongly correlated transition metal oxides: an XMCD insight into the modifications of the magnetic properties of Cr-doped manganites and the structural deformation in nickel perovskites under high applied pressure.Facultad de Ciencias ExactasCentro de Química Inorgánic

Automatic Choroid Layer Segmentation from Optical Coherence Tomography Images Using Deep Learning

The choroid layer is a vascular layer in human retina and its main function is to provide oxygen and support to the retina. Various studies have shown that the thickness of the choroid layer is correlated with the diagnosis of several ophthalmic diseases. For example, diabetic macular edema (DME) is a leading cause of vision loss in patients with diabetes. Despite contemporary advances, automatic segmentation of the choroid layer remains a challenging task due to low contrast, inhomogeneous intensity, inconsistent texture and ambiguous boundaries between the choroid and sclera in Optical Coherence Tomography (OCT) images. The majority of currently implemented methods manually or semi-automatically segment out the region of interest. While many fully automatic methods exist in the context of choroid layer segmentation, more effective and accurate automatic methods are required in order to employ these methods in the clinical sector. This paper proposed and implemented an automatic method for choroid layer segmentation in OCT images using deep learning and a series of morphological operations. The aim of this research was to segment out Bruch’s Membrane (BM) and choroid layer to calculate the thickness map. BM was segmented using a series of morphological operations, whereas the choroid layer was segmented using a deep learning approach as more image statistics were required to segment accurately. Several evaluation metrics were used to test and compare the proposed method against other existing methodologies. Experimental results showed that the proposed method greatly reduced the error rate when compared with the other state-of-the art methods