Classification of SD-OCT volumes with multi pyramids, LBP and HOG descriptors: application to DME detections

International audienceThis paper deals with the automated detection of DME on OCT volumes.Our method considers a generic classification pipeline with preprocessing for noise removal and flattening of each B-Scan.Features such as HoG and LBP are extracted and combined to create a set of different feature vectors which are fed to a linear-SVM classifier.Experimental results show a promising sensitivity/specificity of 0.75/0.87 on a challenging dataset

Dual-Tree Complex Wavelet Input Transform for Cyst Segmentation in OCT Images Based on a Deep Learning Framework

Optical coherence tomography (OCT) represents a non-invasive, high-resolution cross-sectional imaging modality. Macular edema is the swelling of the macular region. Segmentation of fluid or cyst regions in OCT images is essential, to provide useful information for clinicians and prevent visual impairment. However, manual segmentation of fluid regions is a time-consuming and subjective procedure. Traditional and off-the-shelf deep learning methods fail to extract the exact location of the boundaries under complicated conditions, such as with high noise levels and blurred edges. Therefore, developing a tailored automatic image segmentation method that exhibits good numerical and visual performance is essential for clinical application. The dual-tree complex wavelet transform (DTCWT) can extract rich information from different orientations of image boundaries and extract details that improve OCT fluid semantic segmentation results in difficult conditions. This paper presents a comparative study of using DTCWT subbands in the segmentation of fluids. To the best of our knowledge, no previous studies have focused on the various combinations of wavelet transforms and the role of each subband in OCT cyst segmentation. In this paper, we propose a semantic segmentation composite architecture based on a novel U-net and information from DTCWT subbands. We compare different combination schemes, to take advantage of hidden information in the subbands, and demonstrate the performance of the methods under original and noise-added conditions. Dice score, Jaccard index, and qualitative results are used to assess the performance of the subbands. The combination of subbands yielded high Dice and Jaccard values, outperforming the other methods, especially in the presence of a high level of noise

Intraretinal Fluid Pattern Characterization in Optical Coherence Tomography Images

[Abstract] Optical Coherence Tomography (OCT) has become a relevant image modality in the ophthalmological clinical practice, as it offers a detailed representation of the eye fundus. This medical imaging modality is currently one of the main means of identification and characterization of intraretinal cystoid regions, a crucial task in the diagnosis of exudative macular disease or macular edema, among the main causes of blindness in developed countries. This work presents an exhaustive analysis of intensity and texture-based descriptors for its identification and classification, using a complete set of 510 texture features, three state-of-the-art feature selection strategies, and seven representative classifier strategies. The methodology validation and the analysis were performed using an image dataset of 83 OCT scans. From these images, 1609 samples were extracted from both cystoid and non-cystoid regions. The different tested configurations provided satisfactory results, reaching a mean cross-validation test accuracy of 92.69%. The most promising feature categories identified for the issue were the Gabor filters, the Histogram of Oriented Gradients (HOG), the Gray-Level Run-Length matrix (GLRL), and the Laws’ texture filters (LAWS), being consistently and considerably selected along all feature selector algorithms in the top positions of different relevance rankings.Xunta de Galicia; ED431C 2016-047Xunta de Galicia; ED481A-2019/196This 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. Also, 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 and the Xunta de Galicia predoctoral grant contract ref. ED481A-2019/196

Automatic macular edema identification and characterization using OCT images

© 2018. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/. This version of the article: Samagaio, G., Estévez, A., Moura, J. de, Novo, J., Fernández, M. I., & Ortega, M. (2018). “Automatic macular edema identification and characterization using OCT images” has been accepted for publication in Computer Methods and Programs in Biomedicine, 163, 47–63. The Version of Record is available online at: https://doi.org/10.1016/j.cmpb.2018.05.033.[Abstract]: Background and objective: The detection and characterization of the intraretinal fluid accumulation constitutes a crucial ophthalmological issue as it provides useful information for the identification and diagnosis of the different types of Macular Edema (ME). These types are clinically defined, according to the clinical guidelines, as: Serous Retinal Detachment (SRD), Diffuse Retinal Thickening (DRT) and Cystoid Macular Edema (CME). Their accurate identification and characterization facilitate the diagnostic process, determining the disease severity and, therefore, allowing the clinicians to achieve more precise analysis and suitable treatments. Methods: This paper proposes a new fully automatic system for the identification and characterization of the three types of ME using Optical Coherence Tomography (OCT) images. In the case of SRD and CME edemas, multilevel image thresholding approaches were designed and combined with the application of ad-hoc clinical restrictions. The case of DRT edemas, given their complexity and fuzzy regional appearance, was approached by a learning strategy that exploits intensity, texture and clinical-based information to identify their presence. Results: The system provided satisfactory results with F-Measures of 87.54% and 91.99% for the DRT and CME detections, respectively. In the case of SRD edemas, the system correctly detected all the cases that were included in the designed dataset. Conclusions: The proposed methodology offered an accurate performance for the individual identification and characterization of the three different types of ME in OCT images. In fact, the method is capable to handle the ME analysis even in cases of significant severity with the simultaneous existence of the three ME types that appear merged inside the retinal layers.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

Feature Definition and Comprehensive Analysis on the Robust Identification of Intraretinal Cystoid Regions Using Optical Coherence Tomography Images

Financiado para publicación en acceso aberto: Universidade da Coruña/CISUG[Abstract] Currently, optical coherence tomography is one of the most used medical imaging modalities, offering cross-sectional representations of the studied tissues. This image modality is specially relevant for the analysis of the retina, since it is the internal part of the human body that allows an almost direct examination without invasive techniques. One of the most representative cases of use of this medical imaging modality is for the identification and characterization of intraretinal fluid accumulations, critical for the diagnosis of one of the main causes of blindness in developed countries: the Diabetic Macular Edema. The study of these fluid accumulations is particularly interesting, both from the point of view of pattern recognition and from the different branches of health sciences. As these fluid accumulations are intermingled with retinal tissues, they present numerous variants according to their severity, and change their appearance depending on the configuration of the device; they are a perfect subject for an in-depth research, as they are considered to be a problem without a strict solution. In this work, we propose a comprehensive and detailed analysis of the patterns that characterize them. We employed a pool of 11 different texture and intensity feature families (giving a total of 510 markers) which we have analyzed using three different feature selection strategies and seven complementary classification algorithms. By doing so, we have been able to narrow down and explain the factors affecting this kind of accumulations and tissue lesions by means of machine learning techniques with a pipeline specially designed for this purpose.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, Ayudas para la formación de profesorado universitario (FPU), grant ref. FPU18/02271; 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, Grupos de Referencia Competitiva, grant ref. ED431C 2020/24 and through the postdoctoral grant contract ref. ED481B 2021/059; 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%). Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. Funding for open access charge: Universidade da Coruña/CISUGXunta de Galicia; ED431C 2020/24Xunta de Galicia; ED481B 2021/059Xunta de Galicia; IN845D 2020/38Xunta de Galicia; ED431G 2019/0

A new convolutional neural network based on combination of circlets and wavelets for macular OCT classification

Artificial intelligence (AI) algorithms, encompassing machine learning and deep learning, can assist ophthalmologists in early detection of various ocular abnormalities through the analysis of retinal optical coherence tomography (OCT) images. Despite considerable progress in these algorithms, several limitations persist in medical imaging fields, where a lack of data is a common issue. Accordingly, specific image processing techniques, such as time–frequency transforms, can be employed in conjunction with AI algorithms to enhance diagnostic accuracy. This research investigates the influence of non-data-adaptive time–frequency transforms, specifically X-lets, on the classification of OCT B-scans. For this purpose, each B-scan was transformed using every considered X-let individually, and all the sub-bands were utilized as the input for a designed 2D Convolutional Neural Network (CNN) to extract optimal features, which were subsequently fed to the classifiers. Evaluating per-class accuracy shows that the use of the 2D Discrete Wavelet Transform (2D-DWT) yields superior outcomes for normal cases, whereas the circlet transform outperforms other X-lets for abnormal cases characterized by circles in their retinal structure (due to the accumulation of fluid). As a result, we propose a novel transform named CircWave by concatenating all sub-bands from the 2D-DWT and the circlet transform. The objective is to enhance the per-class accuracy of both normal and abnormal cases simultaneously. Our findings show that classification results based on the CircWave transform outperform those derived from original images or any individual transform. Furthermore, Grad-CAM class activation visualization for B-scans reconstructed from CircWave sub-bands highlights a greater emphasis on circular formations in abnormal cases and straight lines in normal cases, in contrast to the focus on irrelevant regions in original B-scans. To assess the generalizability of our method, we applied it to another dataset obtained from a different imaging system. We achieved promising accuracies of 94.5% and 90% for the first and second datasets, respectively, which are comparable with results from previous studies. The proposed CNN based on CircWave sub-bands (i.e. CircWaveNet) not only produces superior outcomes but also offers more interpretable results with a heightened focus on features crucial for ophthalmologists

On orthogonal projections for dimension reduction and applications in augmented target loss functions for learning problems

The use of orthogonal projections on high-dimensional input and target data in learning frameworks is studied. First, we investigate the relations between two standard objectives in dimension reduction, preservation of variance and of pairwise relative distances. Investigations of their asymptotic correlation as well as numerical experiments show that a projection does usually not satisfy both objectives at once. In a standard classification problem we determine projections on the input data that balance the objectives and compare subsequent results. Next, we extend our application of orthogonal projections to deep learning tasks and introduce a general framework of augmented target loss functions. These loss functions integrate additional information via transformations and projections of the target data. In two supervised learning problems, clinical image segmentation and music information classification, the application of our proposed augmented target loss functions increase the accuracy