Joint segmentation and classification of retinal arteries/veins from fundus images

Objective Automatic artery/vein (A/V) segmentation from fundus images is required to track blood vessel changes occurring with many pathologies including retinopathy and cardiovascular pathologies. One of the clinical measures that quantifies vessel changes is the arterio-venous ratio (AVR) which represents the ratio between artery and vein diameters. This measure significantly depends on the accuracy of vessel segmentation and classification into arteries and veins. This paper proposes a fast, novel method for semantic A/V segmentation combining deep learning and graph propagation. Methods A convolutional neural network (CNN) is proposed to jointly segment and classify vessels into arteries and veins. The initial CNN labeling is propagated through a graph representation of the retinal vasculature, whose nodes are defined as the vessel branches and edges are weighted by the cost of linking pairs of branches. To efficiently propagate the labels, the graph is simplified into its minimum spanning tree. Results The method achieves an accuracy of 94.8% for vessels segmentation. The A/V classification achieves a specificity of 92.9% with a sensitivity of 93.7% on the CT-DRIVE database compared to the state-of-the-art-specificity and sensitivity, both of 91.7%. Conclusion The results show that our method outperforms the leading previous works on a public dataset for A/V classification and is by far the fastest. Significance The proposed global AVR calculated on the whole fundus image using our automatic A/V segmentation method can better track vessel changes associated to diabetic retinopathy than the standard local AVR calculated only around the optic disc.Comment: Preprint accepted in Artificial Intelligence in Medicin

Retinal Vascular Network Topology Reconstruction and Artery/Vein Classification via Dominant Set Clustering

The estimation of vascular network topology in complex networks is important in understanding the relationship between vascular changes and a wide spectrum of diseases. Automatic classification of the retinal vascular trees into arteries and veins is of direct assistance to the ophthalmologist in terms of diagnosis and treatment of eye disease. However, it is challenging due to their projective ambiguity and subtle changes in appearance, contrast and geometry in the imaging process. In this paper, we propose a novel method that is capable of making the artery/vein (A/V) distinction in retinal color fundus images based on vascular network topological properties. To this end, we adapt the concept of dominant set clustering and formalize the retinal blood vessel topology estimation and the A/V classification as a pairwise clustering problem. The graph is constructed through image segmentation, skeletonization and identification of significant nodes. The edge weight is defined as the inverse Euclidean distance between its two end points in the feature space of intensity, orientation, curvature, diameter, and entropy. The reconstructed vascular network is classified into arteries and veins based on their intensity and morphology. The proposed approach has been applied to five public databases, INSPIRE, IOSTAR, VICAVR, DRIVE and WIDE, and achieved high accuracies of 95.1%, 94.2%, 93.8%, 91.1%, and 91.0%, respectively. Furthermore, we have made manual annotations of the blood vessel topologies for INSPIRE, IOSTAR, VICAVR, and DRIVE datasets, and these annotations are released for public access so as to facilitate researchers in the community

Retinal Artery/Vein Classification via Graph Cut Optimization

In many diseases with a cardiovascular component, the geometry of microvascular blood vessels changes. These changes are specific to arteries and veins, and can be studied in the microvasculature of the retina using retinal photography. To facilitate large-scale studies of artery/vein-specific changes in the retinal vasculature, automated classification of the vessels is required. Here we present a novel method for artery/vein classification based on local and contextual feature analysis of retinal vessels. For each vessel, local information in the form of a transverse intensity profile is extracted. Crossings and bifurcations of vessels provide contextual information. The local and contextual features are integrated into a non-submodular energy function, which is optimized exactly using graph cuts. The method was validated on a ground truth data set of 150 retinal fundus images, achieving an accuracy of 88.0% for all vessels and 94.0% for the six arteries and six veins with highest caliber in the image

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

Digital ocular fundus imaging: a review

Ocular fundus imaging plays a key role in monitoring the health status of the human eye. Currently, a large number of imaging modalities allow the assessment and/or quantification of ocular changes from a healthy status. This review focuses on the main digital fundus imaging modality, color fundus photography, with a brief overview of complementary techniques, such as fluorescein angiography. While focusing on two-dimensional color fundus photography, the authors address the evolution from nondigital to digital imaging and its impact on diagnosis. They also compare several studies performed along the transitional path of this technology. Retinal image processing and analysis, automated disease detection and identification of the stage of diabetic retinopathy (DR) are addressed as well. The authors emphasize the problems of image segmentation, focusing on the major landmark structures of the ocular fundus: the vascular network, optic disk and the fovea. Several proposed approaches for the automatic detection of signs of disease onset and progression, such as microaneurysms, are surveyed. A thorough comparison is conducted among different studies with regard to the number of eyes/subjects, imaging modality, fundus camera used, field of view and image resolution to identify the large variation in characteristics from one study to another. Similarly, the main features of the proposed classifications and algorithms for the automatic detection of DR are compared, thereby addressing computer-aided diagnosis and computer-aided detection for use in screening programs.Fundação para a Ciência e TecnologiaFEDErPrograma COMPET

Semaphorin 3d Signaling in Cardiovascular Development

Development of the heart is an intricate and complex process. Crucial to this process is vascular patterning and the signals that properly guide developing vessels. Consequences of improper patterning can be severe, including life-threatening congenital heart defects. In this dissertation, I investigate the role of the secreted guidance molecule semaphorin 3d (Sema3d) in cardiovascular patterning during development, and attempt to dissect the molecular mechanisms involved in Sema3d signaling. Using loss-of-function genetic experiments in mice, I model multiple forms of congenital heart defects such as total anomalous pulmonary venous connections, transposition of the great arteries, and congenital abnormalities of the coronary vessels. These mouse models are powerful tools, which I use to investigate the etiology and morphogenesis of these disorders. Critical to understanding these congenital defects in these models is precisely deciphering the cellular and molecular mechanisms involved. I show how Sema3d affects the motility, migration, and adhesion of endothelial cells through a process of cytoskeletal reorganization, and I identify multiple molecules in the Sema3d signaling pathway, including a novel holoreceptor comprised of the receptor tyrosine kinase ErbB2 and semaphorin receptor neuropilin 1. Elucidating the precise mechanisms of normal vascular development along with pathologic processes is a necessary step towards future interventions and possible therapeutics