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

Deep Learning in Cardiology

The medical field is creating large amount of data that physicians are unable to decipher and use efficiently. Moreover, rule-based expert systems are inefficient in solving complicated medical tasks or for creating insights using big data. Deep learning has emerged as a more accurate and effective technology in a wide range of medical problems such as diagnosis, prediction and intervention. Deep learning is a representation learning method that consists of layers that transform the data non-linearly, thus, revealing hierarchical relationships and structures. In this review we survey deep learning application papers that use structured data, signal and imaging modalities from cardiology. We discuss the advantages and limitations of applying deep learning in cardiology that also apply in medicine in general, while proposing certain directions as the most viable for clinical use.Comment: 27 pages, 2 figures, 10 table

Optical imaging of MHD bubble flow in Hele-Shaw liquid metal cells

As a simple and affordable alternative to often prohibitively expensive or unavailable X-ray and neutron imaging, an improved optical imaging method for bubble flow in Hele-Shaw liquid metal cells is presented, enabling measurements with a significantly greater liquid metal layer thickness than previously reported. This enables studying bubble dynamics with varying degrees of geometric confinement, without or with applied magnetic field. The main principles and the experiment setup, as well as the necessary image/data processing pipeline are described, and preliminary results show that the proposed methods can be used to quantify the effects of varying gas flow rate and magnetic field configuration on bubble chain flow in a Hele-Shaw cell

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Is the Vascular Network Discriminant Enough to Classify Renal Cell Carcinoma?

International audienceThe renal cell carcinoma (RCC) is the most frequent type of kidney cancer (between 90% and 95%). Twelve subtypes of RCC can be distinguished, among which the clear cell carcinoma (ccRCC) and the papillary carcinoma (pRCC) are the two most common ones (75% and 10% of the cases, respectively). After resection (i.e., surgical removal), the tumor is prepared for histological examination (fixation, slicing, staining, observation with a microscope). Along with protein expression and genetic tests, the histological study allows to classify the tumor and define its grade in order to make a prognosis and to take decisions for a potential additional chemotherapy treatment. Digital histology is a recent domain, since routinely, histological slices are studied directly under the microscope. The pioneer works deal with the automatic analysis of cells. However, a crucial factor for RCC classification is the tumoral architecture relying on the structure of the vascular network. For example, coarsely speaking, ccRCC is characterized by a ``fishnet'' structure while the pRCC has a tree-like structure. To our knowledge, no computerized analysis of the vascular network has been proposed yet. In this context, we developed a complete pipeline to extract the vascular network of a given histological slice and compute features of the underlying graph structure. Then, we studied the potential of such a feature-based approach in classifying a tumor into ccRCC or pRCC. Preliminary results on patient data are encouraging

Vessel tractography using an intensity based tensor model with branch detection

In this paper, we present a tubular structure seg- mentation method that utilizes a second order tensor constructed from directional intensity measurements, which is inspired from diffusion tensor image (DTI) modeling. The constructed anisotropic tensor which is fit inside a vessel drives the segmen- tation analogously to a tractography approach in DTI. Our model is initialized at a single seed point and is capable of capturing whole vessel trees by an automatic branch detection algorithm developed in the same framework. The centerline of the vessel as well as its thickness is extracted. Performance results within the Rotterdam Coronary Artery Algorithm Evaluation framework are provided for comparison with existing techniques. 96.4% average overlap with ground truth delineated by experts is obtained in addition to other measures reported in the paper. Moreover, we demonstrate further quantitative results over synthetic vascular datasets, and we provide quantitative experiments for branch detection on patient Computed Tomography Angiography (CTA) volumes, as well as qualitative evaluations on the same CTA datasets, from visual scores by a cardiologist expert

Customizable tubular model for n-furcating blood vessels and its application to 3D reconstruction of the cerebrovascular system

Understanding the 3D cerebral vascular network is one of the pressing issues impacting the diagnostics of various systemic disorders and is helpful in clinical therapeutic strategies. Unfortunately, the existing software in the radiological workstation does not meet the expectations of radiologists who require a computerized system for detailed, quantitative analysis of the human cerebrovascular system in 3D and a standardized geometric description of its components. In this study, we show a method that uses 3D image data from magnetic resonance imaging with contrast to create a geometrical reconstruction of the vessels and a parametric description of the reconstructed segments of the vessels. First, the method isolates the vascular system using controlled morphological growing and performs skeleton extraction and optimization. Then, around the optimized skeleton branches, it creates tubular objects optimized for quality and accuracy of matching with the originally isolated vascular data. Finally, it optimizes the joints on n-furcating vessel segments. As a result, the algorithm gives a complete description of shape, position in space, position relative to other segments, and other anatomical structures of each cerebrovascular system segment. Our method is highly customizable and in principle allows reconstructing vascular structures from any 2D or 3D data. The algorithm solves shortcomings of currently available methods including failures to reconstruct the vessel mesh in the proximity of junctions and is free of mesh collisions in high curvature vessels. It also introduces a number of optimizations in the vessel skeletonization leading to a more smooth and more accurate model of the vessel network. We have tested the method on 20 datasets from the public magnetic resonance angiography image database and show that the method allows for repeatable and robust segmentation of the vessel network and allows to compute vascular lateralization indices. Graphical abstract: [Figure not available: see fulltext.]</p

Knife Edge Scanning Microscope Brain Atlas Interface for Tracing and Analysis of Vasculature Data

The study of the neurovascular network in the brain is important to understand brain functions as well as causes of several brain dysfunctions. Many techniques have been applied to acquire neurovascular data. The Knife-Edge Scanning Microscope (KESM), developed by the Brain Network Lab at Texas A&M University, can generate whole-brain-scale data at submicrometer resolution. The specimen can be stained with different stains, and depending on the type of stain used, the KESM can image different types of microstructures in the brain. The India ink stain allows the neurovascular network in the brain to be imaged. In order to visualize and analyze such large datasets (~ 1.5 TB per brain), a lightweight, web-based mouse brain atlas called the Knife-Edge Scanning Microscope Brain Atlas (KESMBA) was developed in the lab. The atlas serves several whole mouse brain data sets including India ink. The multi-section overlay technique used in the atlas enables 3D visualization of the structural information in the data. To solve the challenging issue of tracing micro-vessels in the brain, in this thesis a semi-automated tracing and analysis method is developed and integrated into the KESM brain atlas. Using the KESMBA interface developed in this thesis, the user can look at the 3D structure of the vessels on the brain atlas and can guide the tracing algorithm. To analyze the vasculature network traced by the user, a data analysis component is also added. This new KESMBA interface is expected to help in quickly tracing and analyzing the vascular network of the brain with minimal manual effort. In order to visualize and analyze such large data sets (~ 1.5 TB per brain), a light-weight, web-based mouse brain atlas called the Knife-Edge Scanning Microscope Brain Atlas (KESMBA) was developed in the lab. The atlas serves several whole mouse brain data sets including India ink. The multi-section overlay technique used in the atlas enables 3D visualization of the structural information in the data. To solve the challenging issue of tracing micro-vessels in the brain, in this thesis a semi-automated tracing and analysis method is developed and integrated into the KESM brain atlas. Using the KESMBA interface developed in this thesis, the user can look at the 3D structure of the vessels on the brain atlas and can guide the tracing algorithm. In order to analyze the vasculature network traced by the user, a data analysis component is also added. This new KESMBA interface is expected to help in quickly tracing and analyzing the vascular network of the brain with minimal manual effort

Accurate Image Analysis of the Retina Using Hessian Matrix and Binarisation of Thresholded Entropy with Application of Texture Mapping

In this paper, we demonstrate a comprehensive method for segmenting the retinal vasculature in camera images of the fundus. This is of interest in the area of diagnostics for eye diseases that affect the blood vessels in the eye. In a departure from other state-of-the-art methods, vessels are first pre-grouped together with graph partitioning, using a spectral clustering technique based on morphological features. Local curvature is estimated over the whole image using eigenvalues of Hessian matrix in order to enhance the vessels, which appear as ridges in images of the retina. The result is combined with a binarized image, obtained using a threshold that maximizes entropy, to extract the retinal vessels from the background. Speckle type noise is reduced by applying a connectivity constraint on the extracted curvature based enhanced image. This constraint is varied over the image according to each region's predominant blood vessel size. The resultant image exhibits the central light reflex of retinal arteries and veins, which prevents the segmentation of whole vessels. To address this, the earlier entropy-based binarization technique is repeated on the original image, but crucially, with a different threshold to incorporate the central reflex vessels. The final segmentation is achieved by combining the segmented vessels with and without central light reflex. We carry out our approach on DRIVE and REVIEW, two publicly available collections of retinal images for research purposes. The obtained results are compared with state-of-the-art methods in the literature using metrics such as sensitivity (true positive rate), selectivity (false positive rate) and accuracy rates for the DRIVE images and measured vessel widths for the REVIEW images. Our approach out-performs the methods in the literature.Xiaoxia Yin, Brian W-H Ng, Jing He, Yanchun Zhang, Derek Abbot