Automatic Identification and Representation of the Cornea–Contact Lens Relationship Using AS-OCT Images

[Abstract] The clinical study of the cornea–contact lens relationship is widely used in the process of adaptation of the scleral contact lens (SCL) to the ocular morphology of patients. In that sense, the measurement of the adjustment between the SCL and the cornea can be used to study the comfort or potential damage that the lens may produce in the eye. The current analysis procedure implies the manual inspection of optical coherence tomography of the anterior segment images (AS-OCT) by the clinical experts. This process presents several limitations such as the inability to obtain complex metrics, the inaccuracies of the manual measurements or the requirement of a time-consuming process by the expert in a tedious process, among others. This work proposes a fully-automatic methodology for the extraction of the areas of interest in the study of the cornea–contact lens relationship and the measurement of representative metrics that allow the clinicians to measure quantitatively the adjustment between the lens and the eye. In particular, three distance metrics are herein proposed: Vertical, normal to the tangent of the region of interest and by the nearest point. Moreover, the images are classified to characterize the analysis as belonging to the central cornea, peripheral cornea, limbus or sclera (regions where the inner layer of the lens has already joined the cornea). Finally, the methodology graphically presents the results of the identified segmentations using an intuitive visualization that facilitates the analysis and diagnosis of the patients by the clinical experts.This work is supported by the Instituto de Salud Carlos III, Government of Spain and FEDER funds of the European Union through the DTS18/00136 research projects and by the Ministerio de Ciencia, Innovación y Universidades, Government of Spain through the DPI2015-69948-R and RTI2018-095894-B-I00 research projects. Moreover, this work has received financial support from the European Union (European Regional Development Fund—ERDF) and the Xunta de Galicia, Grupos de Referencia Competitiva, Ref. ED431C 2016-047.Xunta de Galicia; ED431C 2016-047

Enhanced visualization of the retinal vasculature using depth information in OCT

This version of the article has been accepted for publication, after peer review and is subject to Springer Nature’s AM terms of use, but is not the Version of Record and does not reflect post-acceptance improvements, or any corrections. The Version of Record is available online at: https://doi.org/10.1007/s11517-017-1660-8[Abstract]: Retinal vessel tree extraction is a crucial step for analyzing the microcirculation, a frequently needed process in the study of relevant diseases. To date, this has normally been done by using 2D image capture paradigms, offering a restricted visualization of the real layout of the retinal vasculature. In this work, we propose a new approach that automatically segments and reconstructs the 3D retinal vessel tree by combining near-infrared reflectance retinography information with Optical Coherence Tomography (OCT) sections. Our proposal identifies the vessels, estimates their calibers, and obtains the depth at all the positions of the entire vessel tree, thereby enabling the reconstruction of the 3D layout of the complete arteriovenous tree for subsequent analysis. The method was tested using 991 OCT images combined with their corresponding near-infrared reflectance retinography. The different stages of the methodology were validated using the opinion of an expert as a reference. The tests offered accurate results, showing coherent reconstructions of the 3D vasculature that can be analyzed in the diagnosis of relevant diseases affecting the retinal microcirculation, such as hypertension or diabetes, among others.This work is supported by the Instituto de Salud Carlos III, Government of Spain and FEDER funds of the European Union through the PI14/02161 and the DTS15/00153 research projects and by the Ministerio de Economía y Competitividad, Government of Spain through the DPI2015-69948-R research project. Also, this work has received financial support from the European Union (European Regional Development Fund - ERDF) and the Xunta de Galicia, Centro singular de investigación de Galicia accreditation 2016-2019, Ref. ED431G/01; and Grupos de Referencia Competitiva, Ref. ED431C 2016-047.Xunta de Galicia; ED431G/01Xunta de Galicia; ED431C 2016-04

Automatic Segmentation and Intuitive Visualisation of the Epiretinal Membrane in 3D OCT Images Using Deep Convolutional Approaches

[Abstract] Epiretinal Membrane (ERM) is a disease caused by a thin layer of scar tissue that is formed on the surface of the retina. When this membrane appears over the macula, it can cause distorted or blurred vision. Although normally idiopathic, its presence can also be indicative of other pathologies such as diabetic macular edema or vitreous haemorrhage. ERM removal surgery can preserve more visual acuity the earlier it is performed. For this purpose, we present a fully automatic segmentation system that can help the clinicians to determine the ERM presence and location over the eye fundus using 3D Optical Coherence Tomography (OCT) volumes. The proposed system uses a convolutional neural network architecture to classify patches of the retina surface. All the 2D OCT slices of the 3D OCT volume of a patient are combined to produce an intuitive colour map over the 2D fundus reconstruction, providing a visual representation of the presence of ERM which therefore facilitates the diagnosis and treatment of this relevant eye disease. A total of 2.428 2D OCT slices obtained from 20 OCT 3D volumes was used in this work. To validate the designed methodology, several representative experiments were performed. We obtained satisfactory results with a Dice Coefficient of 0.826 ± 0.112 and a Jaccard Index of 0.714 ± 0.155, proving its applicability for diagnosis purposes. The proposed system also demonstrated its simplicity and competitive performance with respect to other state-of-the-art approaches.10.13039/501100004587-Instituto de Salud Carlos III, Government of Spain, research project (Grant Number: DTS18/00136), 10.13039/501100004837-Ministerio de Ciencia e Innovación y Universidades, Government of Spain, research project (Grant Number: RTI2018-095894-B-I00), 10.13039/501100004837-Ministerio de Ciencia e Innovación, Government of Spain through the research project (Grant Number: PID2019-108435RB-I00), 10.13039/501100008425-Consellería de Cultura, Educación e Universidade, Xunta de Galicia, Grupos de Referencia Competitiva (Grant Number: ED431C 2020/24), 10.13039/501100010769-Axencia Galega de Innovación (GAIN), Xunta de Galicia (Grant Number: IN845D 2020/38), 10.13039/501100008425-CITIC, Centro de Investigación de Galicia, receives financial support from the Consellería de Educación, Universidade e Formación Profesional, Xunta de Galicia, through the ERDF (80%) and Secretaría Xeral de Universidades (20%) (Grant Number: ED431G 2019/01)Xunta de Galicia; ED431C 2020/24Xunta de Galicia; IN845D 2020/38Xunta de Galicia; ED431G 2019/0

Automatic Identification and Characterization of the Epiretinal Membrane in OCT Images

[Abstract] Optical coherence tomography (OCT) is a medical image modality that is used to capture, non-invasively, high-resolution cross-sectional images of the retinal tissue. These images constitute a suitable scenario for the diagnosis of relevant eye diseases like the vitreomacular traction or the diabetic retinopathy. The identification of the epiretinal membrane (ERM) is a relevant issue as its presence constitutes a symptom of diseases like the macular edema, deteriorating the vision quality of the patients. This work presents an automatic methodology for the identification of the ERM presence in OCT scans. Initially, a complete and heterogeneous set of features was defined to capture the properties of the ERM in the OCT scans. Selected features went through a feature selection process to further improve the method efficiency. Additionally, representative classifiers were trained and tested to measure the suitability of the proposed approach. The method was tested with a dataset of 285 OCT scans labeled by a specialist. In particular, 3,600 samples were equally extracted from the dataset, representing zones with and without ERM presence. Different experiments were conducted to reach the most suitable approach. Finally, selected classifiers were trained and compared using different metrics, providing in the best configuration an accuracy of 89.35%.Ministerio de Economía, Industria y Competitividad, Gobierno de España (DPI2015-69948-R); Consellería de Cultura, Educación e Ordenación Universitaria, Xunta de Galicia (ED431C 2016-047, ED431G/01); Instituto de Salud Carlos III (ISCIII) (DTS18/00136).Xunta de Galicia; ED431C 2016-047Xunta de Galicia; ED431G/0

Automatic Identification and Intuitive Map Representation of the Epiretinal Membrane Presence in 3D OCT Volumes

[Abstract] Optical Coherence Tomography (OCT) is a medical image modality providing high-resolution cross-sectional visualizations of the retinal tissues without any invasive procedure, commonly used in the analysis of retinal diseases such as diabetic retinopathy or retinal detachment. Early identification of the epiretinal membrane (ERM) facilitates ERM surgical removal operations. Moreover, presence of the ERM is linked to other retinal pathologies, such as macular edemas, being among the main causes of vision loss. In this work, we propose an automatic method for the characterization and visualization of the ERM’s presence using 3D OCT volumes. A set of 452 features is refined using the Spatial Uniform ReliefF (SURF) selection strategy to identify the most relevant ones. Afterwards, a set of representative classifiers is trained, selecting the most proficient model, generating a 2D reconstruction of the ERM’s presence. Finally, a post-processing stage using a set of morphological operators is performed to improve the quality of the generated maps. To verify the proposed methodology, we used 20 3D OCT volumes, both with and without the ERM’s presence, totalling 2428 OCT images manually labeled by a specialist. The most optimal classifier in the training stage achieved a mean accuracy of 91.9%. Regarding the post-processing stage, mean specificity values of 91.9% and 99.0% were obtained from volumes with and without the ERM’s presence, respectively.This work is supported by the Instituto de Salud Carlos III, Government of Spain and FEDER funds of the European Union through the DTS18/00136 research projects and by the Ministerio de Ciencia, Innovación y Universidades, Government of Spain through the DPI2015-69948-R and RTI2018-095894-B-I00 research projects. Moreover, this work has received financial support from the European Union (European Regional Development Fund—ERDF) and the Xunta de Galicia, Grupos de Referencia Competitiva, Ref. ED431C 2016-047.Xunta de Galicia; ED431C 2016-04

Artery/Vein Vessel Tree Identification in Near-Infrared Reflectance Retinographies

This version of the article has been accepted for publication, after peer review and is subject to Springer Nature’s AM terms of use, but is not the Version of Record and does not reflect post-acceptance improvements, or any corrections. The Version of Record is available online at: https://doi.org/10.1007/s10278-019-00235-x[Abstract]: An accurate identification of the retinal arteries and veins is a relevant issue in the development of automatic computer-aided diagnosis systems that facilitate the analysis of different relevant diseases that affect the vascular system as diabetes or hypertension, among others. The proposed method offers a complete analysis of the retinal vascular tree structure by its identification and posterior classification into arteries and veins using optical coherence tomography (OCT) scans. These scans include the near-infrared reflectance retinography images, the ones we used in this work, in combination with the corresponding histological sections. The method, firstly, segments the vessel tree and identifies its characteristic points. Then, Global Intensity-Based Features (GIBS) are used to measure the differences in the intensity profiles between arteries and veins. A k-means clustering classifier employs these features to evaluate the potential of artery/vein identification of the proposed method. Finally, a post-processing stage is applied to correct misclassifications using context information and maximize the performance of the classification process. The methodology was validated using an OCT image dataset retrieved from 46 different patients, where 2,392 vessel segments and 97,294 vessel points were manually labeled by an expert clinician. The method achieved satisfactory results, reaching a best accuracy of 93.35% in the identification of arteries and veins, being the first proposal that faces this issue in this image modality.This work is supported by the Instituto de Salud Carlos III, Government of Spain and FEDER funds of the European Union through the DTS18/00136 research project and by the Ministerio de Economía y Competitividad, Government of Spain through the DPI2015-69948-R research project. Also, this work has received financial support from the European Union (European Regional Development Fund—ERDF); the Xunta de Galicia, Centro singular de investigación de Galicia accreditation 2016–2019, Ref. ED431G/01; and Grupos de Referencia Competitiva, Ref. ED431C 2016-047.Xunta de Galicia; ED431G/01Xunta de Galicia; ED431C 2016-04

Automatic Segmentation and Visualisation of the Epirretinal Membrane in OCT Scans Using Densely Connected Convolutional Networks

Presented at the 4th XoveTIC Conference, A Coruña, Spain, 7–8 October 2021.[Abstract] The Epiretinal Membrane (ERM) is an ocular disease that appears as a fibro-cellular layer of tissue over the retina, specifically, over the Inner Limiting Membrane (ILM). It causes vision blurring and distortion, and its presence can be indicative of other ocular pathologies, such as diabetic macular edema. The ERM diagnosis is usually performed by visually inspecting Optical Coherence Tomography (OCT) images, a manual process which is tiresome and prone to subjectivity. In this work, we present a methodology for the automatic segmentation and visualisation of the ERM in OCT volumes using deep learning. By employing a Densely Connected Convolutional Network, every pixel in the ILM can be classified into either healthy or pathological. Thus, a segmentation of the region susceptible to ERM appearance can be produced. This methodology also produces an intuitive colour map representation of the ERM presence over a visualisation of the eye fundus created from the OCT volume. In a series of representative experiments conducted to evaluate this methodology, it achieved a Dice score of 0.826±0.112 and a Jaccard index of 0.714±0.155. The results that were obtained demonstrate the competitive performance of the proposed methodology when compared to other works in the state of the art.This research was funded by Instituto de Salud Carlos III, Government of Spain, DTS18/00136 research project; Ministerio de Ciencia e Innovación y Universidades, Government of Spain, RTI2018-095894-B-I00 research project; Ministerio de Ciencia e Innovación, Government of Spain through the research project with reference PID2019-108435RB-I00; Consellería de Cultura, Educación e Universidade, Xunta de Galicia through the predoctoral and postdoctoral grant contracts ref. ED481A 2021/161 and ED481B 2021/059, respectively; and Grupos de Referencia Competitiva, grant ref. ED431C 2020/24; Axencia Galega de Innovación (GAIN), Xunta de Galicia, grant ref. IN845D 2020/38; CITIC, Centro de Investigación de Galicia ref. ED431G 2019/01, receives financial support from Consellería de Educación, Universidade e Formación Profesional, Xunta de Galicia, through the ERDF (80%) and Secretaría Xeral de Universidades (20%)Xunta de Galicia; ED481A 2021/161Xunta de Galicia; ED481B 2021/059Xunta de Galicia; ED431C 2020/24Xunta de Galicia; IN845D 2020/38Xunta de Galicia; ED431G 2019/0

Retinal Vascular Analysis in a Fully Automated Method for the Segmentation of DRT Edemas Using OCT Images

[Abstract] Optical Coherence Tomography (OCT) is a well-established medical imaging technique that allows a complete analysis and evaluation of the main retinal structures and their histopathology properties. Diabetic Macular Edema (DME) implies the accumulation of intraretinal fluid within the macular region. Diffuse Retinal Thickening (DRT) edemas are considered a relevant case of DME disease, where the pathological regions are characterized by a “sponge-like” appearance and a reduced intraretinal reflectivity, being visible in OCT images. Additionally, the presence of other structures may alter the OCT image characteristics, confusing the pathological identification process. This is the case of the retinal vessels over all the eye fundus, whose presence produce shadow projections over the retinal layers that may hide the “sponge-like” appearance of the DRT edemas. Thus, in this paper, we present a proposal for the automatic extraction of DRT edemas, also using as reference the information provided by the automatic identifications of the retinal vessels in the OCT images. To do that, firstly, the system delimits three retinal regions of interest. These retinal regions facilitate the posterior identification of the vessel structures and the segmentation of the DRT regions. For the identification of the vessels structures, the method combined the localization of the upper bright vascular profiles with the presence of their corresponding lower dark vascular shadows. Finally, a learning strategy is implemented for the segmentation of the DRT edemas. Satisfactory results were obtained, reaching values of 0.8346 and 0.9051 of Jaccard index and Dice coefficient, respectively, for the extraction of the existing DRT edemas.Xunta de Galicia; ED431G/01Xunta de Galicia; ED431C 2016-047This work is supported by the Instituto de Salud Carlos III, Government of Spain and FEDER funds of the European Union through the DTS18/00136 research projects and by the Ministerio de Economía y Competitividad, Government of Spain through the DPI2015-69948-R research project. Also, this work has received financial support from the European Union (European Regional Development Fund - ERDF) and the Xunta de Galicia, Centro singular de investigación de Galicia accreditation 2016-2019, Ref. ED431G/01; and Grupos de Referencia Competitiva, Ref. ED431C 2016-047

Improvement of Retinal Images Affected by Cataracts

Eye fundus images are used in clinical diagnosis for the detection and assessment of retinal disorders. When retinal images are degraded by scattering due to opacities of the eye tissues, the precise detection of abnormalities is complicated depending on the grading of the opacity. This paper presents a concept proof study on the use of the contrast limited adaptive histogram equalization (CLAHE) technique for better visualization of eye fundus images for different levels of blurring due to different stages of cataracts. Processing is performed in three different color spaces: RGB, CIELAB and HSV, with the aim of finding which one better enhances the missed diagnostic features due to blur. The experimental results show that some fundus features not observable by naked eye can be detected in some of the space color processed with the proposed method. In this work, we also develop and provide an online image process, which allows clinicians to tune the default parameters of the algorithm for a better visualization of the characteristics of fundus images. It also allows the choice of a region of interest (ROI) within the images that provide better visualization of some features than those enhanced by the processing of the full picture