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

Force field feature extraction for ear biometrics

The overall objective in defining feature space is to reduce the dimensionality of the original pattern space, whilst maintaining discriminatory power for classification. To meet this objective in the context of ear biometrics a new force field transformation treats the image as an array of mutually attracting particles that act as the source of a Gaussian force field. Underlying the force field there is a scalar potential energy field, which in the case of an ear takes the form of a smooth surface that resembles a small mountain with a number of peaks joined by ridges. The peaks correspond to potential energy wells and to extend the analogy the ridges correspond to potential energy channels. Since the transform also turns out to be invertible, and since the surface is otherwise smooth, information theory suggests that much of the information is transferred to these features, thus confirming their efficacy. We previously described how field line feature extraction, using an algorithm similar to gradient descent, exploits the directional properties of the force field to automatically locate these channels and wells, which then form the basis of characteristic ear features. We now show how an analysis of the mechanism of this algorithmic approach leads to a closed analytical description based on the divergence of force direction, which reveals that channels and wells are really manifestations of the same phenomenon. We further show that this new operator, with its own distinct advantages, has a striking similarity to the Marr-Hildreth operator, but with the important difference that it is non-linear. As well as addressing faster implementation, invertibility, and brightness sensitivity, the technique is also validated by performing recognition on a database of ears selected from the XM2VTS face database, and by comparing the results with the more established technique of Principal Components Analysis. This confirms not only that ears do indeed appear to have potential as a biometric, but also that the new approach is well suited to their description, being robust especially in the presence of noise, and having the advantage that the ear does not need to be explicitly extracted from the background

Singular solutions, momentum maps and computational anatomy

This paper describes the variational formulation of template matching problems of computational anatomy (CA); introduces the EPDiff evolution equation in the context of an analogy between CA and fluid dynamics; discusses the singular solutions for the EPDiff equation and explains why these singular solutions exist (singular momentum map). Then it draws the consequences of EPDiff for outline matching problem in CA and gives numerical examples