Information-Theoretic Registration with Explicit Reorientation of Diffusion-Weighted Images

We present an information-theoretic approach to the registration of images with directional information, and especially for diffusion-Weighted Images (DWI), with explicit optimization over the directional scale. We call it Locally Orderless Registration with Directions (LORD). We focus on normalized mutual information as a robust information-theoretic similarity measure for DWI. The framework is an extension of the LOR-DWI density-based hierarchical scale-space model that varies and optimizes the integration, spatial, directional, and intensity scales. As affine transformations are insufficient for inter-subject registration, we extend the model to non-rigid deformations. We illustrate that the proposed model deforms orientation distribution functions (ODFs) correctly and is capable of handling the classic complex challenges in DWI-registrations, such as the registration of fiber-crossings along with kissing, fanning, and interleaving fibers. Our experimental results clearly illustrate a novel promising regularizing effect, that comes from the nonlinear orientation-based cost function. We show the properties of the different image scales and, we show that including orientational information in our model makes the model better at retrieving deformations in contrast to standard scalar-based registration.Comment: 16 pages, 19 figure

On the use of SIFT features for face authentication

Several pattern recognition and classification techniques have been applied to the biometrics domain. Among them, an interesting technique is the Scale Invariant Feature Transform (SIFT), originally devised for object recognition. Even if SIFT features have emerged as a very powerful image descriptors, their employment in face analysis context has never been systematically investigated. This paper investigates the application of the SIFT approach in the context of face authentication. In order to determine the real potential and applicability of the method, different matching schemes are proposed and tested using the BANCA database and protocol, showing promising results

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

Geometry Processing of Conventionally Produced Mouse Brain Slice Images

Brain mapping research in most neuroanatomical laboratories relies on conventional processing techniques, which often introduce histological artifacts such as tissue tears and tissue loss. In this paper we present techniques and algorithms for automatic registration and 3D reconstruction of conventionally produced mouse brain slices in a standardized atlas space. This is achieved first by constructing a virtual 3D mouse brain model from annotated slices of Allen Reference Atlas (ARA). Virtual re-slicing of the reconstructed model generates ARA-based slice images corresponding to the microscopic images of histological brain sections. These image pairs are aligned using a geometric approach through contour images. Histological artifacts in the microscopic images are detected and removed using Constrained Delaunay Triangulation before performing global alignment. Finally, non-linear registration is performed by solving Laplace's equation with Dirichlet boundary conditions. Our methods provide significant improvements over previously reported registration techniques for the tested slices in 3D space, especially on slices with significant histological artifacts. Further, as an application we count the number of neurons in various anatomical regions using a dataset of 51 microscopic slices from a single mouse brain. This work represents a significant contribution to this subfield of neuroscience as it provides tools to neuroanatomist for analyzing and processing histological data.Comment: 14 pages, 11 figure

Alignment of contrast enhanced medical images

The re-alignment of series of medical images in which there are multiple contrast variations is difficult. The reason for this is that the popularmeasures of image similarity used to drive the alignment procedure do not separate the influence of intensity variation due to image feature motion and intensity variation due to feature enhancement. In particular, the appearance of new structure poses problems when it has no representation in the original image. The acquisition of many images over time, such as in dynamic contrast enhanced MRI, requires that many images with different contrast be registered to the same coordinate system, compounding the problem. This thesis addresses these issues, beginning by presenting conditions under which conventional registration fails and proposing a solution in the form of a ’progressive principal component registration’. The algorithm uses a statistical analysis of a series of contrast varying images in order to reduce the influence of contrast-enhancement that would otherwise distort the calculation of the image similarity measures used in image registration. The algorithm is shown to be versatile in that it may be applied to series of images in which contrast variation is due to either temporal contrast enhancement changes, as in dynamic contrast-enhanced MRI or intrinsically in the image selection procedure as in diffusion weighted MRI

The accuracy of ADC measurements in liver is improved by a tailored and computationally efficient local-rigid registration algorithm

This study describes post-processing methodologies to reduce the effects of physiological motion in measurements of apparent diffusion coefficient (ADC) in the liver. The aims of the study are to improve the accuracy of ADC measurements in liver disease to support quantitative clinical characterisation and reduce the number of patients required for sequential studies of disease progression and therapeutic effects. Two motion correction methods are compared, one based on non-rigid registration (NRA) using freely available open source algorithms and the other a local-rigid registration (LRA) specifically designed for use with diffusion weighted magnetic resonance (DW-MR) data. Performance of these methods is evaluated using metrics computed from regional ADC histograms on abdominal image slices from healthy volunteers. While the non-rigid registration method has the advantages of being applicable on the whole volume and in a fully automatic fashion, the local-rigid registration method is faster while maintaining the integrity of the biological structures essential for analysis of tissue heterogeneity. Our findings also indicate that the averaging commonly applied to DW-MR images as part of the acquisition protocol should be avoided if possible

See the Difference: Direct Pre-Image Reconstruction and Pose Estimation by Differentiating HOG

The Histogram of Oriented Gradient (HOG) descriptor has led to many advances in computer vision over the last decade and is still part of many state of the art approaches. We realize that the associated feature computation is piecewise differentiable and therefore many pipelines which build on HOG can be made differentiable. This lends to advanced introspection as well as opportunities for end-to-end optimization. We present our implementation of $\nabla$HOG based on the auto-differentiation toolbox Chumpy and show applications to pre-image visualization and pose estimation which extends the existing differentiable renderer OpenDR pipeline. Both applications improve on the respective state-of-the-art HOG approaches