Fast Multi-frame Stereo Scene Flow with Motion Segmentation

We propose a new multi-frame method for efficiently computing scene flow (dense depth and optical flow) and camera ego-motion for a dynamic scene observed from a moving stereo camera rig. Our technique also segments out moving objects from the rigid scene. In our method, we first estimate the disparity map and the 6-DOF camera motion using stereo matching and visual odometry. We then identify regions inconsistent with the estimated camera motion and compute per-pixel optical flow only at these regions. This flow proposal is fused with the camera motion-based flow proposal using fusion moves to obtain the final optical flow and motion segmentation. This unified framework benefits all four tasks - stereo, optical flow, visual odometry and motion segmentation leading to overall higher accuracy and efficiency. Our method is currently ranked third on the KITTI 2015 scene flow benchmark. Furthermore, our CPU implementation runs in 2-3 seconds per frame which is 1-3 orders of magnitude faster than the top six methods. We also report a thorough evaluation on challenging Sintel sequences with fast camera and object motion, where our method consistently outperforms OSF [Menze and Geiger, 2015], which is currently ranked second on the KITTI benchmark.Comment: 15 pages. To appear at IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2017). Our results were submitted to KITTI 2015 Stereo Scene Flow Benchmark in November 201

Online Mutual Foreground Segmentation for Multispectral Stereo Videos

The segmentation of video sequences into foreground and background regions is a low-level process commonly used in video content analysis and smart surveillance applications. Using a multispectral camera setup can improve this process by providing more diverse data to help identify objects despite adverse imaging conditions. The registration of several data sources is however not trivial if the appearance of objects produced by each sensor differs substantially. This problem is further complicated when parallax effects cannot be ignored when using close-range stereo pairs. In this work, we present a new method to simultaneously tackle multispectral segmentation and stereo registration. Using an iterative procedure, we estimate the labeling result for one problem using the provisional result of the other. Our approach is based on the alternating minimization of two energy functions that are linked through the use of dynamic priors. We rely on the integration of shape and appearance cues to find proper multispectral correspondences, and to properly segment objects in low contrast regions. We also formulate our model as a frame processing pipeline using higher order terms to improve the temporal coherence of our results. Our method is evaluated under different configurations on multiple multispectral datasets, and our implementation is available online.Comment: Preprint accepted for publication in IJCV (December 2018

Inferring Geodesic Cerebrovascular Graphs: Image Processing, Topological Alignment and Biomarkers Extraction

A vectorial representation of the vascular network that embodies quantitative features - location, direction, scale, and bifurcations - has many potential neuro-vascular applications. Patient-specific models support computer-assisted surgical procedures in neurovascular interventions, while analyses on multiple subjects are essential for group-level studies on which clinical prediction and therapeutic inference ultimately depend. This first motivated the development of a variety of methods to segment the cerebrovascular system. Nonetheless, a number of limitations, ranging from data-driven inhomogeneities, the anatomical intra- and inter-subject variability, the lack of exhaustive ground-truth, the need for operator-dependent processing pipelines, and the highly non-linear vascular domain, still make the automatic inference of the cerebrovascular topology an open problem. In this thesis, brain vessels’ topology is inferred by focusing on their connectedness. With a novel framework, the brain vasculature is recovered from 3D angiographies by solving a connectivity-optimised anisotropic level-set over a voxel-wise tensor field representing the orientation of the underlying vasculature. Assuming vessels joining by minimal paths, a connectivity paradigm is formulated to automatically determine the vascular topology as an over-connected geodesic graph. Ultimately, deep-brain vascular structures are extracted with geodesic minimum spanning trees. The inferred topologies are then aligned with similar ones for labelling and propagating information over a non-linear vectorial domain, where the branching pattern of a set of vessels transcends a subject-specific quantized grid. Using a multi-source embedding of a vascular graph, the pairwise registration of topologies is performed with the state-of-the-art graph matching techniques employed in computer vision. Functional biomarkers are determined over the neurovascular graphs with two complementary approaches. Efficient approximations of blood flow and pressure drop account for autoregulation and compensation mechanisms in the whole network in presence of perturbations, using lumped-parameters analog-equivalents from clinical angiographies. Also, a localised NURBS-based parametrisation of bifurcations is introduced to model fluid-solid interactions by means of hemodynamic simulations using an isogeometric analysis framework, where both geometry and solution profile at the interface share the same homogeneous domain. Experimental results on synthetic and clinical angiographies validated the proposed formulations. Perspectives and future works are discussed for the group-wise alignment of cerebrovascular topologies over a population, towards defining cerebrovascular atlases, and for further topological optimisation strategies and risk prediction models for therapeutic inference. Most of the algorithms presented in this work are available as part of the open-source package VTrails

Segmentation of pelvic structures from preoperative images for surgical planning and guidance

Prostate cancer is one of the most frequently diagnosed malignancies globally and the second leading cause of cancer-related mortality in males in the developed world. In recent decades, many techniques have been proposed for prostate cancer diagnosis and treatment. With the development of imaging technologies such as CT and MRI, image-guided procedures have become increasingly important as a means to improve clinical outcomes. Analysis of the preoperative images and construction of 3D models prior to treatment would help doctors to better localize and visualize the structures of interest, plan the procedure, diagnose disease and guide the surgery or therapy. This requires efficient and robust medical image analysis and segmentation technologies to be developed. The thesis mainly focuses on the development of segmentation techniques in pelvic MRI for image-guided robotic-assisted laparoscopic radical prostatectomy and external-beam radiation therapy. A fully automated multi-atlas framework is proposed for bony pelvis segmentation in MRI, using the guidance of MRI AE-SDM. With the guidance of the AE-SDM, a multi-atlas segmentation algorithm is used to delineate the bony pelvis in a new \ac{MRI} where there is no CT available. The proposed technique outperforms state-of-the-art algorithms for MRI bony pelvis segmentation. With the SDM of pelvis and its segmented surface, an accurate 3D pelvimetry system is designed and implemented to measure a comprehensive set of pelvic geometric parameters for the examination of the relationship between these parameters and the difficulty of robotic-assisted laparoscopic radical prostatectomy. This system can be used in both manual and automated manner with a user-friendly interface. A fully automated and robust multi-atlas based segmentation has also been developed to delineate the prostate in diagnostic MR scans, which have large variation in both intensity and shape of prostate. Two image analysis techniques are proposed, including patch-based label fusion with local appearance-specific atlases and multi-atlas propagation via a manifold graph on a database of both labeled and unlabeled images when limited labeled atlases are available. The proposed techniques can achieve more robust and accurate segmentation results than other multi-atlas based methods. The seminal vesicles are also an interesting structure for therapy planning, particularly for external-beam radiation therapy. As existing methods fail for the very onerous task of segmenting the seminal vesicles, a multi-atlas learning framework via random decision forests with graph cuts refinement has further been proposed to solve this difficult problem. Motivated by the performance of this technique, I further extend the multi-atlas learning to segment the prostate fully automatically using multispectral (T1 and T2-weighted) MR images via hybrid \ac{RF} classifiers and a multi-image graph cuts technique. The proposed method compares favorably to the previously proposed multi-atlas based prostate segmentation. The work in this thesis covers different techniques for pelvic image segmentation in MRI. These techniques have been continually developed and refined, and their application to different specific problems shows ever more promising results.Open Acces

Image segmentation with adaptive region growing based on a polynomial surface model

A new method for segmenting intensity images into smooth surface segments is presented. The main idea is to divide the image into flat, planar, convex, concave, and saddle patches that coincide as well as possible with meaningful object features in the image. Therefore, we propose an adaptive region growing algorithm based on low-degree polynomial fitting. The algorithm uses a new adaptive thresholding technique with the L∞ fitting cost as a segmentation criterion. The polynomial degree and the fitting error are automatically adapted during the region growing process. The main contribution is that the algorithm detects outliers and edges, distinguishes between strong and smooth intensity transitions and finds surface segments that are bent in a certain way. As a result, the surface segments corresponding to meaningful object features and the contours separating the surface segments coincide with real-image object edges. Moreover, the curvature-based surface shape information facilitates many tasks in image analysis, such as object recognition performed on the polynomial representation. The polynomial representation provides good image approximation while preserving all the necessary details of the objects in the reconstructed images. The method outperforms existing techniques when segmenting images of objects with diffuse reflecting surfaces

RGB-D Scene Representations for Prosthetic Vision

This thesis presents a new approach to scene representation for prosthetic vision. Structurally salient information from the scene is conveyed through the prosthetic vision display. Given the low resolution and dynamic range of the display, this enables robust identification and reliable interpretation of key structural features that are missed when using standard appearance-based scene representations. Specifically, two different types of salient structure are investigated: salient edge structure, for depiction of scene shape to the user; and salient object structure, for emulation of biological attention deployment when viewing a scene. This thesis proposes and evaluates novel computer vision algorithms for extracting salient edge and salient object structure from RGB-D input. Extraction of salient edge structure from the scene is first investigated through low-level analysis of surface shape. Our approach is based on the observation that regions of irregular surface shape, such as the boundary between the wall and the floor, tend to be more informative of scene structure than uniformly shaped regions. We detect these surface irregularities through multi-scale analysis of iso-disparity contour orientations, providing a real time method that robustly identifies important scene structure. This approach is then extended by using a deep CNN to learn high level information for distinguishing salient edges from structural texture. A novel depth input encoding called the depth surface descriptor (DSD) is presented, which better captures scene geometry that corresponds to salient edges, improving the learned model. These methods provide robust detection of salient edge structure in the scene. The detection of salient object structure is first achieved by noting that salient objects often have contrasting shape from their surroundings. Contrasting shape in the depth image is captured through the proposed histogram of surface orientations (HOSO) feature. This feature is used to modulate depth and colour contrast in a saliency detection framework, improving the precision of saliency seed regions and through this the accuracy of the final detection. After this, a novel formulation of structural saliency is introduced based on the angular measure of local background enclosure (LBE). This formulation addresses fundamental limitations of depth contrast methods and is not reliant on foreground depth contrast in the scene. Saliency is instead measured through the degree to which a candidate patch exhibits foreground structure. The effectiveness of the proposed approach is evaluated through both standard datasets as well as user studies that measure the contribution of structure-based representations. Our methods are found to more effectively measure salient structure in the scene than existing methods. Our approach results in improved performance compared to standard methods during practical use of an implant display

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