Fast Predictive Image Registration

We present a method to predict image deformations based on patch-wise image appearance. Specifically, we design a patch-based deep encoder-decoder network which learns the pixel/voxel-wise mapping between image appearance and registration parameters. Our approach can predict general deformation parameterizations, however, we focus on the large deformation diffeomorphic metric mapping (LDDMM) registration model. By predicting the LDDMM momentum-parameterization we retain the desirable theoretical properties of LDDMM, while reducing computation time by orders of magnitude: combined with patch pruning, we achieve a 1500x/66x speed up compared to GPU-based optimization for 2D/3D image registration. Our approach has better prediction accuracy than predicting deformation or velocity fields and results in diffeomorphic transformations. Additionally, we create a Bayesian probabilistic version of our network, which allows evaluation of deformation field uncertainty through Monte Carlo sampling using dropout at test time. We show that deformation uncertainty highlights areas of ambiguous deformations. We test our method on the OASIS brain image dataset in 2D and 3D

Interactive Medical Image Registration With Multigrid Methods and Bounded Biharmonic Functions

Interactive image registration is important in some medical applications since automatic image registration is often slow and sometimes error-prone. We consider interactive registration methods that incorporate user-specified local transforms around control handles. The deformation between handles is interpolated by some smooth functions, minimizing some variational energies. Besides smoothness, we expect the impact of a control handle to be local. Therefore we choose bounded biharmonic weight functions to blend local transforms, a cutting-edge technique in computer graphics. However, medical images are usually huge, and this technique takes a lot of time that makes itself impracticable for interactive image registration. To expedite this process, we use a multigrid active set method to solve bounded biharmonic functions (BBF). The multigrid approach is for two scenarios, refining the active set from coarse to fine resolutions, and solving the linear systems constrained by working active sets. We\u27ve implemented both weighted Jacobi method and successive over-relaxation (SOR) in the multigrid solver. Since the problem has box constraints, we cannot directly use regular updates in Jacobi and SOR methods. Instead, we choose a descent step size and clamp the update to satisfy the box constraints. We explore the ways to choose step sizes and discuss their relation to the spectral radii of the iteration matrices. The relaxation factors, which are closely related to step sizes, are estimated by analyzing the eigenvalues of the bilaplacian matrices. We give a proof about the termination of our algorithm and provide some theoretical error bounds. Another minor problem we address is to register big images on GPU with limited memory. We\u27ve implemented an image registration algorithm with virtual image slices on GPU. An image slice is treated similarly to a page in virtual memory. We execute a wavefront of subtasks together to reduce the number of data transfers. Our main contribution is a fast multigrid method for interactive medical image registration that uses bounded biharmonic functions to blend local transforms. We report a novel multigrid approach to refine active set quickly and use clamped updates based on weighted Jacobi and SOR. This multigrid method can be used to efficiently solve other quadratic programs that have active sets distributed over continuous regions

Structure from Motion with Higher-level Environment Representations

Computer vision is an important area focusing on understanding, extracting and using the information from vision-based sensor. It has many applications such as vision-based 3D reconstruction, simultaneous localization and mapping(SLAM) and data-driven understanding of the real world. Vision is a fundamental sensing modality in many different fields of application. While the traditional structure from motion mostly uses sparse point-based feature, this thesis aims to explore the possibility of using higher order feature representation. It starts with a joint work which uses straight line for feature representation and performs bundle adjustment with straight line parameterization. Then, we further try an even higher order representation where we use Bezier spline for parameterization. We start with a simple case where all contours are lying on the plane and uses Bezier splines to parametrize the curves in the background and optimize on both camera position and Bezier splines. For application, we present a complete end-to-end pipeline which produces meaningful dense 3D models from natural data of a 3D object: the target object is placed on a structured but unknown planar background that is modeled with splines. The data is captured using only a hand-held monocular camera. However, this application is limited to a planar scenario and we manage to push the parameterizations into real 3D. Following the potential of this idea, we introduce a more flexible higher-order extension of points that provide a general model for structural edges in the environment, no matter if straight or curved. Our model relies on linked B´ezier curves, the geometric intuition of which proves great benefits during parameter initialization and regularization. We present the first fully automatic pipeline that is able to generate spline-based representations without any human supervision. Besides a full graphical formulation of the problem, we introduce both geometric and photometric cues as well as higher-level concepts such overall curve visibility and viewing angle restrictions to automatically manage the correspondences in the graph. Results prove that curve-based structure from motion with splines is able to outperform state-of-the-art sparse feature-based methods, as well as to model curved edges in the environment

Current Approaches for Image Fusion of Histological Data with Computed Tomography and Magnetic Resonance Imaging

Classical analysis of biological samples requires the destruction of the tissue’s integrity by cutting or grinding it down to thin slices for (Immuno)-histochemical staining and microscopic analysis. Despite high specificity, encoded in the stained 2D section of the whole tissue, the structural information, especially 3D information, is limited. Computed tomography (CT) or magnetic resonance imaging (MRI) scans performed prior to sectioning in combination with image registration algorithms provide an opportunity to regain access to morphological characteristics as well as to relate histological findings to the 3D structure of the local tissue environment. This review provides a summary of prevalent literature addressing the problem of multimodal coregistration of hard- and soft-tissue in microscopy and tomography. Grouped according to the complexity of the dimensions, including image-to-volume (2D ⟶ 3D), image-to-image (2D ⟶ 2D), and volume-to-volume (3D ⟶ 3D), selected currently applied approaches are investigated by comparing the method accuracy with respect to the limiting resolution of the tomography. Correlation of multimodal imaging could position itself as a useful tool allowing for precise histological diagnostic and allow the a priori planning of tissue extraction like biopsies