Deep learning for cardiac image segmentation: A review

Deep learning has become the most widely used approach for cardiac image segmentation in recent years. In this paper, we provide a review of over 100 cardiac image segmentation papers using deep learning, which covers common imaging modalities including magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound (US) and major anatomical structures of interest (ventricles, atria and vessels). In addition, a summary of publicly available cardiac image datasets and code repositories are included to provide a base for encouraging reproducible research. Finally, we discuss the challenges and limitations with current deep learning-based approaches (scarcity of labels, model generalizability across different domains, interpretability) and suggest potential directions for future research

CNN for IMU Assisted Odometry Estimation using Velodyne LiDAR

We introduce a novel method for odometry estimation using convolutional neural networks from 3D LiDAR scans. The original sparse data are encoded into 2D matrices for the training of proposed networks and for the prediction. Our networks show significantly better precision in the estimation of translational motion parameters comparing with state of the art method LOAM, while achieving real-time performance. Together with IMU support, high quality odometry estimation and LiDAR data registration is realized. Moreover, we propose alternative CNNs trained for the prediction of rotational motion parameters while achieving results also comparable with state of the art. The proposed method can replace wheel encoders in odometry estimation or supplement missing GPS data, when the GNSS signal absents (e.g. during the indoor mapping). Our solution brings real-time performance and precision which are useful to provide online preview of the mapping results and verification of the map completeness in real time

Automated liver tissues delineation based on machine learning techniques: A survey, current trends and future orientations

There is no denying how machine learning and computer vision have grown in the recent years. Their highest advantages lie within their automation, suitability, and ability to generate astounding results in a matter of seconds in a reproducible manner. This is aided by the ubiquitous advancements reached in the computing capabilities of current graphical processing units and the highly efficient implementation of such techniques. Hence, in this paper, we survey the key studies that are published between 2014 and 2020, showcasing the different machine learning algorithms researchers have used to segment the liver, hepatic-tumors, and hepatic-vasculature structures. We divide the surveyed studies based on the tissue of interest (hepatic-parenchyma, hepatic-tumors, or hepatic-vessels), highlighting the studies that tackle more than one task simultaneously. Additionally, the machine learning algorithms are classified as either supervised or unsupervised, and further partitioned if the amount of works that fall under a certain scheme is significant. Moreover, different datasets and challenges found in literature and websites, containing masks of the aforementioned tissues, are thoroughly discussed, highlighting the organizers original contributions, and those of other researchers. Also, the metrics that are used excessively in literature are mentioned in our review stressing their relevancy to the task at hand. Finally, critical challenges and future directions are emphasized for innovative researchers to tackle, exposing gaps that need addressing such as the scarcity of many studies on the vessels segmentation challenge, and why their absence needs to be dealt with in an accelerated manner.Comment: 41 pages, 4 figures, 13 equations, 1 table. A review paper on liver tissues segmentation based on automated ML-based technique

Lidar-based scene understanding for autonomous driving using deep learning

With over 1.35 million fatalities related to traffic accidents worldwide, autonomous driving was foreseen at the beginning of this century as a feasible solution to improve security in our roads. Nevertheless, it is meant to disrupt our transportation paradigm, allowing to reduce congestion, pollution, and costs, while increasing the accessibility, efficiency, and reliability of the transportation for both people and goods. Although some advances have gradually been transferred into commercial vehicles in the way of Advanced Driving Assistance Systems (ADAS) such as adaptive cruise control, blind spot detection or automatic parking, however, the technology is far from mature. A full understanding of the scene is actually needed so that allowing the vehicles to be aware of the surroundings, knowing the existing elements of the scene, as well as their motion, intentions and interactions. In this PhD dissertation, we explore new approaches for understanding driving scenes from 3D LiDAR point clouds by using Deep Learning methods. To this end, in Part I we analyze the scene from a static perspective using independent frames to detect the neighboring vehicles. Next, in Part II we develop new ways for understanding the dynamics of the scene. Finally, in Part III we apply all the developed methods to accomplish higher level challenges such as segmenting moving obstacles while obtaining their rigid motion vector over the ground. More specifically, in Chapter 2 we develop a 3D vehicle detection pipeline based on a multi-branch deep-learning architecture and propose a Front (FR-V) and a Bird’s Eye view (BE-V) as 2D representations of the 3D point cloud to serve as input for training our models. Later on, in Chapter 3 we apply and further test this method on two real uses-cases, for pre-filtering moving obstacles while creating maps to better localize ourselves on subsequent days, as well as for vehicle tracking. From the dynamic perspective, in Chapter 4 we learn from the 3D point cloud a novel dynamic feature that resembles optical flow from RGB images. For that, we develop a new approach to leverage RGB optical flow as pseudo ground truth for training purposes but allowing the use of only 3D LiDAR data at inference time. Additionally, in Chapter 5 we explore the benefits of combining classification and regression learning problems to face the optical flow estimation task in a joint coarse-and-fine manner. Lastly, in Chapter 6 we gather the previous methods and demonstrate that with these independent tasks we can guide the learning of higher challenging problems such as segmentation and motion estimation of moving vehicles from our own moving perspective.Con más de 1,35 millones de muertes por accidentes de tráfico en el mundo, a principios de siglo se predijo que la conducción autónoma sería una solución viable para mejorar la seguridad en nuestras carreteras. Además la conducción autónoma está destinada a cambiar nuestros paradigmas de transporte, permitiendo reducir la congestión del tráfico, la contaminación y el coste, a la vez que aumentando la accesibilidad, la eficiencia y confiabilidad del transporte tanto de personas como de mercancías. Aunque algunos avances, como el control de crucero adaptativo, la detección de puntos ciegos o el estacionamiento automático, se han transferido gradualmente a vehículos comerciales en la forma de los Sistemas Avanzados de Asistencia a la Conducción (ADAS), la tecnología aún no ha alcanzado el suficiente grado de madurez. Se necesita una comprensión completa de la escena para que los vehículos puedan entender el entorno, detectando los elementos presentes, así como su movimiento, intenciones e interacciones. En la presente tesis doctoral, exploramos nuevos enfoques para comprender escenarios de conducción utilizando nubes de puntos en 3D capturadas con sensores LiDAR, para lo cual empleamos métodos de aprendizaje profundo. Con este fin, en la Parte I analizamos la escena desde una perspectiva estática para detectar vehículos. A continuación, en la Parte II, desarrollamos nuevas formas de entender las dinámicas del entorno. Finalmente, en la Parte III aplicamos los métodos previamente desarrollados para lograr desafíos de nivel superior, como segmentar obstáculos dinámicos a la vez que estimamos su vector de movimiento sobre el suelo. Específicamente, en el Capítulo 2 detectamos vehículos en 3D creando una arquitectura de aprendizaje profundo de dos ramas y proponemos una vista frontal (FR-V) y una vista de pájaro (BE-V) como representaciones 2D de la nube de puntos 3D que sirven como entrada para entrenar nuestros modelos. Más adelante, en el Capítulo 3 aplicamos y probamos aún más este método en dos casos de uso reales, tanto para filtrar obstáculos en movimiento previamente a la creación de mapas sobre los que poder localizarnos mejor en los días posteriores, como para el seguimiento de vehículos. Desde la perspectiva dinámica, en el Capítulo 4 aprendemos de la nube de puntos en 3D una característica dinámica novedosa que se asemeja al flujo óptico sobre imágenes RGB. Para ello, desarrollamos un nuevo enfoque que aprovecha el flujo óptico RGB como pseudo muestras reales para entrenamiento, usando solo information 3D durante la inferencia. Además, en el Capítulo 5 exploramos los beneficios de combinar los aprendizajes de problemas de clasificación y regresión para la tarea de estimación de flujo óptico de manera conjunta. Por último, en el Capítulo 6 reunimos los métodos anteriores y demostramos que con estas tareas independientes podemos guiar el aprendizaje de problemas de más alto nivel, como la segmentación y estimación del movimiento de vehículos desde nuestra propia perspectivaAmb més d’1,35 milions de morts per accidents de trànsit al món, a principis de segle es va predir que la conducció autònoma es convertiria en una solució viable per millorar la seguretat a les nostres carreteres. D’altra banda, la conducció autònoma està destinada a canviar els paradigmes del transport, fent possible així reduir la densitat del trànsit, la contaminació i el cost, alhora que augmentant l’accessibilitat, l’eficiència i la confiança del transport tant de persones com de mercaderies. Encara que alguns avenços, com el control de creuer adaptatiu, la detecció de punts cecs o l’estacionament automàtic, s’han transferit gradualment a vehicles comercials en forma de Sistemes Avançats d’Assistència a la Conducció (ADAS), la tecnologia encara no ha arribat a aconseguir el grau suficient de maduresa. És necessària, doncs, una total comprensió de l’escena de manera que els vehicles puguin entendre l’entorn, detectant els elements presents, així com el seu moviment, intencions i interaccions. A la present tesi doctoral, explorem nous enfocaments per tal de comprendre les diferents escenes de conducció utilitzant núvols de punts en 3D capturats amb sensors LiDAR, mitjançant l’ús de mètodes d’aprenentatge profund. Amb aquest objectiu, a la Part I analitzem l’escena des d’una perspectiva estàtica per a detectar vehicles. A continuació, a la Part II, desenvolupem noves formes d’entendre les dinàmiques de l’entorn. Finalment, a la Part III apliquem els mètodes prèviament desenvolupats per a aconseguir desafiaments d’un nivell superior, com, per exemple, segmentar obstacles dinàmics al mateix temps que estimem el seu vector de moviment respecte al terra. Concretament, al Capítol 2 detectem vehicles en 3D creant una arquitectura d’aprenentatge profund amb dues branques, i proposem una vista frontal (FR-V) i una vista d’ocell (BE-V) com a representacions 2D del núvol de punts 3D que serveixen com a punt de partida per entrenar els nostres models. Més endavant, al Capítol 3 apliquem i provem de nou aquest mètode en dos casos d’ús reals, tant per filtrar obstacles en moviment prèviament a la creació de mapes en els quals poder localitzar-nos millor en dies posteriors, com per dur a terme el seguiment de vehicles. Des de la perspectiva dinàmica, al Capítol 4 aprenem una nova característica dinàmica del núvol de punts en 3D que s’assembla al flux òptic sobre imatges RGB. Per a fer-ho, desenvolupem un nou enfocament que aprofita el flux òptic RGB com pseudo mostres reals per a entrenament, utilitzant només informació 3D durant la inferència. Després, al Capítol 5 explorem els beneficis que s’obtenen de combinar els aprenentatges de problemes de classificació i regressió per la tasca d’estimació de flux òptic de manera conjunta. Finalment, al Capítol 6 posem en comú els mètodes anteriors i demostrem que mitjançant aquests processos independents podem abordar l’aprenentatge de problemes més complexos, com la segmentació i estimació del moviment de vehicles des de la nostra pròpia perspectiva

A deep learning algorithm for contour detection in synthetic 2D biplanar X-ray images of the scapula: towards improved 3D reconstruction of the scapula

Three-dimensional (3D) reconstruction from X-ray images using statistical shape models (SSM) provides a cost-effective way of increasing the diagnostic utility of two-dimensional (2D) X-ray images, especially in low-resource settings. The landmark-constrained model fitting approach is one way to obtain patient-specific models from a statistical model. This approach requires an accurate selection of corresponding features, usually landmarks, from the bi-planar X-ray images. However, X-ray images are 2D representations of 3D anatomy with super-positioned structures, which confounds this approach. The literature shows that detection and use of contours to locate corresponding landmarks within biplanar X-ray images can address this limitation. The aim of this research project was to train and validate a deep learning algorithm for detection the contour of a scapula in synthetic 2D bi-planar Xray images. Synthetic bi-planar X-ray images were obtained from scapula mesh samples with annotated landmarks generated from a validated SSM obtained from the Division of Biomedical Engineering, University of Cape Town. This was followed by the training of two convolutional neural network models as the first objective of the project; the first model was trained to predict the lateral (LAT) scapula image given the anterior-posterior (AP) image. The second model was trained to predict the AP image given the LAT image. The trained models had an average Dice coefficient value of 0.926 and 0.964 for the predicted LAT and AP images, respectively. However, the trained models did not generalise to the segmented real X-ray images of the scapula. The second objective was to perform landmark-constrained model fitting using the corresponding landmarks embedded in the predicted images. To achieve this objective, the 2D landmark locations were transformed into 3D coordinates using the direct linear transformation. The 3D point localization yielded average errors of (0.35, 0.64, 0.72) mm in the X, Y and Z directions, respectively, and a combined coordinate error of 1.16 mm. The reconstructed landmarks were used to reconstruct meshes that had average surface-to-surface distances of 3.22 mm and 1.72 mm for 3 and 6 landmarks, respectively. The third objective was to reconstruct the scapula mesh using matching points on the scapula contour in the bi-planar images. The average surface-to-surface distances of the reconstructed meshes with 8 matching contour points and 6 corresponding landmarks of the same meshes were 1.40 and 1.91 mm, respectively. In summary, the deep learning models were able to learn the mapping between the bi-planar images of the scapula. Increasing the number of corresponding landmarks from the bi-planar images resulted into better 3D reconstructions. However, obtaining these corresponding landmarks was non-trivial, necessitating the use of matching points selected from the scapulae contours. The results from the latter approach signal a need to explore contour matching methods to obtain more corresponding points in order to improve the scapula 3D reconstruction using landmark-constrained model fitting

Deep learning in medical image registration: introduction and survey

Image registration (IR) is a process that deforms images to align them with respect to a reference space, making it easier for medical practitioners to examine various medical images in a standardized reference frame, such as having the same rotation and scale. This document introduces image registration using a simple numeric example. It provides a definition of image registration along with a space-oriented symbolic representation. This review covers various aspects of image transformations, including affine, deformable, invertible, and bidirectional transformations, as well as medical image registration algorithms such as Voxelmorph, Demons, SyN, Iterative Closest Point, and SynthMorph. It also explores atlas-based registration and multistage image registration techniques, including coarse-fine and pyramid approaches. Furthermore, this survey paper discusses medical image registration taxonomies, datasets, evaluation measures, such as correlation-based metrics, segmentation-based metrics, processing time, and model size. It also explores applications in image-guided surgery, motion tracking, and tumor diagnosis. Finally, the document addresses future research directions, including the further development of transformers

Real-Time Magnetic Resonance Imaging

Real‐time magnetic resonance imaging (RT‐MRI) allows for imaging dynamic processes as they occur, without relying on any repetition or synchronization. This is made possible by modern MRI technology such as fast‐switching gradients and parallel imaging. It is compatible with many (but not all) MRI sequences, including spoiled gradient echo, balanced steady‐state free precession, and single‐shot rapid acquisition with relaxation enhancement. RT‐MRI has earned an important role in both diagnostic imaging and image guidance of invasive procedures. Its unique diagnostic value is prominent in areas of the body that undergo substantial and often irregular motion, such as the heart, gastrointestinal system, upper airway vocal tract, and joints. Its value in interventional procedure guidance is prominent for procedures that require multiple forms of soft‐tissue contrast, as well as flow information. In this review, we discuss the history of RT‐MRI, fundamental tradeoffs, enabling technology, established applications, and current trends

Cardiac magnetic resonance assessment of central and peripheral vascular function in patients undergoing renal sympathetic denervation as predictor for blood pressure response

Background: Most trials regarding catheter-based renal sympathetic denervation (RDN) describe a proportion of patients without blood pressure response. Recently, we were able to show arterial stiffness, measured by invasive pulse wave velocity (IPWV), seems to be an excellent predictor for blood pressure response. However, given the invasiveness, IPWV is less suitable as a selection criterion for patients undergoing RDN. Consequently, we aimed to investigate the value of cardiac magnetic resonance (CMR) based measures of arterial stiffness in predicting the outcome of RDN compared to IPWV as reference. Methods: Patients underwent CMR prior to RDN to assess ascending aortic distensibility (AAD), total arterial compliance (TAC), and systemic vascular resistance (SVR). In a second step, central aortic blood pressure was estimated from ascending aortic area change and flow sequences and used to re-calculate total arterial compliance (cTAC). Additionally, IPWV was acquired. Results: Thirty-two patients (24 responders and 8 non-responders) were available for analysis. AAD, TAC and cTAC were higher in responders, IPWV was higher in non-responders. SVR was not different between the groups. Patients with AAD, cTAC or TAC above median and IPWV below median had significantly better BP response. Receiver operating characteristic (ROC) curves predicting blood pressure response for IPWV, AAD, cTAC and TAC revealed areas under the curve of 0.849, 0.828, 0.776 and 0.753 (p = 0.004, 0.006, 0.021 and 0.035). Conclusions: Beyond IPWV, AAD, cTAC and TAC appear as useful outcome predictors for RDN in patients with hypertension. CMR-derived markers of arterial stiffness might serve as non-invasive selection criteria for RDN

Automatic CT Angiography Lesion Segmentation Compared to CT Perfusion in Ischemic Stroke Detection: a Feasibility Study

In stroke imaging, CT angiography (CTA) is used for detecting arterial occlusions. These images could also provide information on the extent of ischemia. The study aim was to develop and evaluate a convolutional neural network (CNN)-based algorithm for detecting and segmenting acute ischemic lesions from CTA images of patients with suspected middle cerebral artery stroke. These results were compared to volumes reported by widely used CT perfusion-based RAPID software (IschemaView). A 42-layer-deep CNN was trained on 50 CTA volumes with manually delineated targets. The lower bound for predicted lesion size to reliably discern stroke from false positives was estimated. The severity of false positives and false negatives was reviewed visually to assess the clinical applicability and to further guide the method development. The CNN model corresponded to the manual segmentations with voxel-wise sensitivity 0.54 (95% confidence interval: 0.44-0.63), precision 0.69 (0.60-0.76), and Sorensen-Dice coefficient 0.61 (0.52-0.67). Stroke/nonstroke differentiation accuracy 0.88 (0.81-0.94) was achieved when only considering the predicted lesion size (i.e., regardless of location). By visual estimation, 46% of cases showed some false findings, such as CNN highlighting chronic periventricular white matter changes or beam hardening artifacts, but only in 9% the errors were severe, translating to 0.91 accuracy. The CNN model had a moderately strong correlation to RAPID-reported T-max > 10 s volumes (Pearson's r = 0.76 (0.58-0.86)). The results suggest that detecting anterior circulation ischemic strokes from CTA using a CNN-based algorithm can be feasible when accompanied with physiological knowledge to rule out false positives.Peer reviewe