0000000000063864
AUTHOR
Carmen Alina Lupascu
Novel VAMPIRE algorithms for quantitative analysis of the retinal vasculature
This paper summarizes three recent, novel algorithms developed within VAMPIRE, namely optic disc and macula detection, arteryvein classification, and enhancement of binary vessel masks, and their performance assessment. VAMPIRE is an international collaboration growing a suite of software tools to allow efficient quantification of morphological properties of the retinal vasculature in large collections of fundus camera images. VAMPIRE measurements are currently mostly used in biomarker research, i.e., investigating associations between the morphology of the retinal vasculature and a number of clinical and cognitive conditions.
Approximated overlap error for the evaluation of feature descriptors on 3D scenes
This paper presents a new framework to evaluate feature descriptors on 3D datasets. The proposed method employs the approximated overlap error in order to conform with the reference planar evaluation case of the Oxford dataset based on the overlap error. The method takes into account not only the keypoint centre but also the feature shape and it does not require complex data setups, depth maps or an accurate camera calibration. Only a ground-truth fundamental matrix should be computed, so that the dataset can be freely extended by adding further images. The proposed approach is robust to false positives occurring in the evaluation process, which do not introduce any relevant changes in the …
VAMPIRE: Vessel assessment and measurement platform for images of the REtina
We present VAMPIRE, a software application for efficient, semi-automatic quantification of retinal vessel properties with large collections of fundus camera images. VAMPIRE is also an international collaborative project of four image processing groups and five clinical centres. The system provides automatic detection of retinal landmarks (optic disc, vasculature), and quantifies key parameters used frequently in investigative studies: vessel width, vessel branching coefficients, and tortuosity. The ultimate vision is to make VAMPIRE available as a public tool, to support quantification and analysis of large collections of fundus camera images.
Stable Automatic Unsupervised Segmentation of Retinal Vessels Using Self-Organizing Maps and a Modified Fuzzy C-Means Clustering
In this paper an automatic unsupervised method for the segmentation of retinal vessels is proposed. Three features are extracted from the tested image. The features are scaled down by a factor of 2 and mapped into a Self-Organizing Map. A modified Fuzzy C-Means clustering algorithm is used to divide the neuron units of the map in 2 classes. The entire image is again input for the Self-Organizing Map and the class of each pixel will be the class of its best matching unit in the Self-Organizing Map. Finally, the vessel network is post-processed using a hill climbing strategy on the connected components of the segmented image. The experimental evaluation on the DRIVE database shows accurate ex…
Graph-based minimal path tracking in the skeleton of the retinal vascular network
This paper presents a semi-automatic framework for minimal path tracking in the skeleton of the retinal vascular network. The method is based on the graph structure of the vessel network. The vascular network is represented based on the skeleton of the available segmented vessels and using an undirected graph. Significant points on the skeleton are considered nodes of the graph, while the edge of the graph is represented by the vessel segment linking two neighboring nodes. The graph is represented then in the form of a connectivity matrix, using a novel method for defining vertex connectivity. Dijkstra and Floyd-Warshall algorithms are applied for detection of minimal paths within the graph…
Analysis of normal human retinal vascular network architecture using multifractal geometry
AIM To apply the multifractal analysis method as a quantitative approach to a comprehensive description of the microvascular network architecture of the normal human retina. METHODS Fifty volunteers were enrolled in this study in the Ophthalmological Clinic of Cluj-Napoca, Romania, between January 2012 and January 2014. A set of 100 segmented and skeletonised human retinal images, corresponding to normal states of the retina were studied. An automatic unsupervised method for retinal vessel segmentation was applied before multifractal analysis. The multifractal analysis of digital retinal images was made with computer algorithms, applying the standard box-counting method. Statistical analyse…
Analysis of low-correlated spatial gene expression patterns: A clustering approach in the mouse brain data hosted in the Allen Brain Atlas
The Allen Brain Atlas (ABA) provides a similar gene expression dataset by genome-scale mapping of the C57BL/6J mouse brain. In this study, the authors describe a method to extract the spatial information of gene expression patterns across a set of 1047 genes. The genes were chosen from among the 4104 genes having the lowest Pearson correlation coefficient used to compare the expression patterns across voxels in a single hemisphere for available coronal and sagittal volumes. The set of genes analysed in this study is the one discarded in the article by Bohland et al. , which was considered to be of a lower consistency, not a reliable dataset. Following a normalisation task with a global and …
Human Visual Perception and Retinal Diseases
Retinal diseases are causing alterations of the visual perception leading sometimes to blindness. For this reason, early detection and diagnosis of retinal pathologies is very important. Using digital image processing techniques, retinal images may be analyzed quickly and computer-assisted diagnosis systems may be developed in order to help the ophthalmologists to make a diagnosis. In this paper we described shortly two computer-assisted systems for the detection of retinal landmarks (optic disc and vasculature) together with a brief introduction to the human visual system and to some alterations of the visual perception caused by retinal diseases.
Semi-automatic registration of retinal images based on line matching approach
Accurate retinal image registration is essential to track the evolution of eye-related diseases. We propose a semiautomatic method based on features relying upon retinal graphs for temporal registration of retinal images. The features represent straight lines connecting vascular landmarks on the retina vascular tree: bifurcations, branchings, crossings, end points. In the built retinal graph, one straight line between two vascular landmarks indicates that they are connected by a vascular segment in the original retinal image. The locations of the landmarks are manually extracted to avoid the information loss due to errors in a retinal vessels segmentation algorithms. A straight line model i…
A non-parametric segmentation methodology for oral videocapillaroscopic images
We aim to describe a new non-parametric methodology to support the clinician during the diagnostic process of oral videocapillaroscopy to evaluate peripheral microcirculation. Our methodology, mainly based on wavelet analysis and mathematical morphology to preprocess the images, segments them by minimizing the within-class luminosity variance of both capillaries and background. Experiments were carried out on a set of real microphotographs to validate this approach versus handmade segmentations provided by physicians. By using a leave-one-patient-out approach, we pointed out that our methodology is robust, according to precision-recall criteria (average precision and recall are equal to 0.9…
Automatic Unsupervised Segmentation of Retinal Vessels Using Self-Organizing Maps and K-Means Clustering
In this paper an automatic unsupervised method for the segmentation of retinal vessels is proposed. A Self-Organizing Map is trained on a portion of the same image that is tested and K-means clustering algorithm is used to divide the map units in 2 classes. The entire image is again input for the Self-Organizing Map, and the class of each pixel will be the class of the best matching unit on the Self-Organizing Map. Finally, the vessel network is post-processed using a hill climbing strategy on the connected components of the segmented image. The experimental evaluation on the publicly available DRIVE database shows accurate extraction of vessels network and a good agreement between our segm…
Blood vessel segmentation and width estimation in ultra-wide field scanning laser ophthalmoscopy.
Features of the retinal vasculature, such as vessel widths, are considered biomarkers for systemic disease. The aim of this work is to present a supervised approach to vessel segmentation in ultra-wide field of view scanning laser ophthalmoscope (UWFoV SLO) images and to evaluate its performance in terms of segmentation and vessel width estimation accuracy. The results of the proposed method are compared with ground truth measurements from human observers and with existing state-of-the-art techniques developed for fundus camera images that we optimized for UWFoV SLO images. Our algorithm is based on multi-scale matched filters, a neural network classifier and hysteresis thresholding. After …
A Comparative Study on Feature Selection for Retinal Vessel Segmentation Using FABC
This paper presents a comparative study on five feature selection heuristics applied to a retinal image database called DRIVE. Features are chosen from a feature vector (encoding local information, but as well information from structures and shapes available in the image) constructed for each pixel in the field of view (FOV) of the image. After selecting the most discriminatory features, an AdaBoost classifier is applied for training. The results of classifications are used to compare the effectiveness of the five feature selection methods.
FABC: Retinal Vessel Segmentation Using AdaBoost
This paper presents a method for automated vessel segmentation in retinal images. For each pixel in the field of view of the image, a 41-D feature vector is constructed, encoding information on the local intensity structure, spatial properties, and geometry at multiple scales. An AdaBoost classifier is trained on 789 914 gold standard examples of vessel and nonvessel pixels, then used for classifying previously unseen images. The algorithm was tested on the public digital retinal images for vessel extraction (DRIVE) set, frequently used in the literature and consisting of 40 manually labeled images with gold standard. Results were compared experimentally with those of eight algorithms as we…
Automated Detection of Optic Disc Location in Retinal Images
This contribution presents an automated method to locate the optic disc in color fundus images. The method uses texture descriptors and a regression based method in order to determine the best circle that fits the optic disc. The best circle is chosen from a set of circles determined with an innovative method, not using the Hough transform as past approaches. An evaluation of the proposed method has been done using a database of 40 images. On this data set, our method achieved 95% success rate for the localization of the optic disc and 70% success rate for the identification of the optic disc contour (as a circle).
A multiscale approach to automatic and unsupervised retinal vessel segmentation using Self-Organizing Maps
In this paper an automatic unsupervised method for retinal vessel segmentation is described. Self-Organizing Map, modified Fuzzy C-Means, STAPLE algorithms and majority voting strategy were adopted to identify a segmentation of the retinal vessels. The performance of the proposed method was evaluated on the DRIVE database.
Flow evaluation of red blood cells in capillaroscopic videos
We aim at describing a non-parametric approach to evaluate blood cells velocity in oral capillascopic videos. The proposed methodology is based on the application of standard optical flow algorithms and it is part of a general environment to support during the diagnostic process for evaluating peripheral microcirculation in real time. We validated our approach versus handmade measurements provided by physicians. Results on real data pointed out that our system returns an output coherent to these latter observations.
Clustering of low-correlated spatial gene expression patterns in the mouse brain in the Allen Brain Atlas
In this paper, clustering techniques are applied to spatial gene expression patterns with a low genomic correlation between the sagittal and coronal projections. The data analysed here are hosted on an available public DB named ABA (Allen Brain Atlas). The results are compared to those obtained by Bohland et al. on the complementary dataset (high correlation values). We prove that, by analysing a reduced dataset,hence reducing the computational burden, we get the same accuracy in highlighting different neuroanatomical region.
Accurate estimation of retinal vessel width using bagged decision trees and an extended multiresolution Hermite model.
We present an algorithm estimating the width of retinal vessels in fundus camera images. The algorithm uses a novel parametric surface model of the cross-sectional intensities of vessels, and ensembles of bagged decision trees to estimate the local width from the parameters of the best-fit surface. We report comparative tests with REVIEW, currently the public database of reference for retinal width estimation, containing 16 images with 193 annotated vessel segments and 5066 profile points annotated manually by three independent experts. Comparative tests are reported also with our own set of 378 vessel widths selected sparsely in 38 images from the Tayside Scotland diabetic retinopathy scre…