Robust RANSAC-based blood vessel segmentation

International audienceMany vascular clinical applications require a vessel segmentation process that is able to both extract the centerline and the surface of the blood vessels. However, noise and topology issues (such as kissing vessels) prevent existing algorithms from being able to easily retrieve such a complex system as the brain vasculature. We propose here a new blood vessel tracking algorithm that 1) detect the vessel centerline; 2) provide a local radius estimate; and 3) extracts a dense set of points at the blood vessel surface. This algorithm is based on a RANSAC-based robust fitting of successive cylinders along the vessel. Our method was validated against the Multiple Hypothesis Testing (MHT) algorithm on 10 3DRA patient data of the brain vasculature. Over 30 blood vessels of various sizes were considered for each patient. Our results demonstrated a greater ability of our algorithm to track small, tortuous and touching vessels (96% success rate), compared to MHT (65% success rate). The computed centerline precision was below 1 voxel when compared to MHT. Moreover, our results were obtained with the same set of parameters for all patients and all blood vessels, except for the seed point for each vessel, also necessary for MHT. The proposed algorithm is thereafter able to extract the full intracranial vasculature with little user interaction

Tram-Line filtering for retinal vessel segmentation

The segmentation of the vascular network from retinal fundal images is a fundamental step in the analysis of the retina, and may be used for a number of purposes, including diagnosis of diabetic retinopathy. However, due to the variability of retinal images segmentation is difficult, particularly with images of diseased retina which include significant distractors. This paper introduces a non-linear filter for vascular segmentation, which is particularly robust against such distractors. We demonstrate results on the publicly-available STARE dataset, superior to Stare’s performance, with 57.2% of the vascular network (by length) successfully located, with 97.2% positive predictive value measured by vessel length, compared with 57% and 92.2% for Stare. The filter is also simple and computationally efficient

Retinal blood vessel segmentation: methods and implementations

Since the retinal blood vessel has been acknowledged as an indispensable element in both ophthalmological and cardiovascular disease diagnosis, the accurate segmentation of the retinal vessel tree has become the prerequisite step for automatic or computer-aided diagnosis systems. This thesis, therefore, has investigated different works of image segmentation algorithms and techniques, including unsupervised and supervised methods. Further, the thesis has developed and implemented two systems of the accurate retinal vessel segmentation. The methodologies explained and analyzed in this thesis, have been selected as the most efficient approaches to achieve higher precision, better robustness, and faster execution speed, to meet the strict standard of the modern medical imaging. Based on the intensive investigation and experiments, this thesis has proposed two outstanding implementations of the retinal blood vessel segmentation. The first implementation focuses on the fast, accurate and robust extraction of the retinal vessels using unsupervised techniques, by applying morphology-based global thresholding to draw the retinal venule structure and centerline detection to extract the capillaries. Besides, this system has been designed to minimize the computing complexity and to process multiple independent procedures in parallel. The second proposed system has especially focused on robustness and accuracy in regardless of execution time. This method has utilized the full convolutional neural network trained from a pre-trained semantic segmentation model, which is also called the transfer deep learning. This proposed method has simplified the typical retinal vessel segmentation problem from full-size image segmentation to regional vessel element recognition. Both of the implementations have outperformed their related works and have presented a remarkable scientific value for future computer-aided diagnosis applications. What’s more, this thesis is also a research guide which provide readers with the comprehensive knowledge on how to research on the task of retinal vessel segmentation

Retinal blood vessel segmentation: methods and implementations

Since the retinal blood vessel has been acknowledged as an indispensable element in both ophthalmological and cardiovascular disease diagnosis, the accurate segmentation of the retinal vessel tree has become the prerequisite step for automatic or computer-aided diagnosis systems. This thesis, therefore, has investigated different works of image segmentation algorithms and techniques, including unsupervised and supervised methods. Further, the thesis has developed and implemented two systems of the accurate retinal vessel segmentation. The methodologies explained and analyzed in this thesis, have been selected as the most efficient approaches to achieve higher precision, better robustness, and faster execution speed, to meet the strict standard of the modern medical imaging. Based on the intensive investigation and experiments, this thesis has proposed two outstanding implementations of the retinal blood vessel segmentation. The first implementation focuses on the fast, accurate and robust extraction of the retinal vessels using unsupervised techniques, by applying morphology-based global thresholding to draw the retinal venule structure and centerline detection to extract the capillaries. Besides, this system has been designed to minimize the computing complexity and to process multiple independent procedures in parallel. The second proposed system has especially focused on robustness and accuracy in regardless of execution time. This method has utilized the full convolutional neural network trained from a pre-trained semantic segmentation model, which is also called the transfer deep learning. This proposed method has simplified the typical retinal vessel segmentation problem from full-size image segmentation to regional vessel element recognition. Both of the implementations have outperformed their related works and have presented a remarkable scientific value for future computer-aided diagnosis applications. What’s more, this thesis is also a research guide which provide readers with the comprehensive knowledge on how to research on the task of retinal vessel segmentation

Retinal blood vessel segmentation: methods and implementations

Since the retinal blood vessel has been acknowledged as an indispensable element in both ophthalmological and cardiovascular disease diagnosis, the accurate segmentation of the retinal vessel tree has become the prerequisite step for automatic or computer-aided diagnosis systems. This thesis, therefore, has investigated different works of image segmentation algorithms and techniques, including unsupervised and supervised methods. Further, the thesis has developed and implemented two systems of the accurate retinal vessel segmentation. The methodologies explained and analyzed in this thesis, have been selected as the most efficient approaches to achieve higher precision, better robustness, and faster execution speed, to meet the strict standard of the modern medical imaging. Based on the intensive investigation and experiments, this thesis has proposed two outstanding implementations of the retinal blood vessel segmentation. The first implementation focuses on the fast, accurate and robust extraction of the retinal vessels using unsupervised techniques, by applying morphology-based global thresholding to draw the retinal venule structure and centerline detection to extract the capillaries. Besides, this system has been designed to minimize the computing complexity and to process multiple independent procedures in parallel. The second proposed system has especially focused on robustness and accuracy in regardless of execution time. This method has utilized the full convolutional neural network trained from a pre-trained semantic segmentation model, which is also called the transfer deep learning. This proposed method has simplified the typical retinal vessel segmentation problem from full-size image segmentation to regional vessel element recognition. Both of the implementations have outperformed their related works and have presented a remarkable scientific value for future computer-aided diagnosis applications. What’s more, this thesis is also a research guide which provide readers with the comprehensive knowledge on how to research on the task of retinal vessel segmentation

Accurate and reliable segmentation of the optic disc in digital fundus images

We describe a complete pipeline for the detection and accurate automatic segmentation of the optic disc in digital fundus images. This procedure provides separation of vascular information and accurate inpainting of vessel-removed images, symmetry-based optic disc localization, and fitting of incrementally complex contour models at increasing resolutions using information related to inpainted images and vessel masks. Validation experiments, performed on a large dataset of images of healthy and pathological eyes, annotated by experts and partially graded with a quality label, demonstrate the good performances of the proposed approach. The method is able to detect the optic disc and trace its contours better than the other systems presented in the literature and tested on the same data. The average error in the obtained contour masks is reasonably close to the interoperator errors and suitable for practical applications. The optic disc segmentation pipeline is currently integrated in a complete software suite for the semiautomatic quantification of retinal vessel properties from fundus camera images (VAMPIRE)

Toward Improving Safety in Neurosurgery with an Active Handheld Instrument

Microsurgical procedures, such as petroclival meningioma resection, require careful surgical actions in order to remove tumor tissue, while avoiding brain and vessel damaging. Such procedures are currently performed under microscope magnification. Robotic tools are emerging in order to filter surgeons’ unintended movements and prevent tools from entering forbidden regions such as vascular structures. The present work investigates the use of a handheld robotic tool (Micron) to automate vessel avoidance in microsurgery. In particular, we focused on vessel segmentation, implementing a deep-learning-based segmentation strategy in microscopy images, and its integration with a feature-based passive 3D reconstruction algorithm to obtain accurate and robust vessel position. We then implemented a virtual-fixture-based strategy to control the handheld robotic tool and perform vessel avoidance. Clay vascular phantoms, lying on a background obtained from microscopy images recorded during petroclival meningioma surgery, were used for testing the segmentation and control algorithms. When testing the segmentation algorithm on 100 different phantom images, a median Dice similarity coefficient equal to 0.96 was achieved. A set of 25 Micron trials of 80 s in duration, each involving the interaction of Micron with a different vascular phantom, were recorded, with a safety distance equal to 2 mm, which was comparable to the median vessel diameter. Micron’s tip entered the forbidden region 24% of the time when the control algorithm was active. However, the median penetration depth was 16.9 μm, which was two orders of magnitude lower than median vessel diameter. Results suggest the system can assist surgeons in performing safe vessel avoidance during neurosurgical procedures