2,054 research outputs found
Part-to-whole Registration of Histology and MRI using Shape Elements
Image registration between histology and magnetic resonance imaging (MRI) is
a challenging task due to differences in structural content and contrast. Too
thick and wide specimens cannot be processed all at once and must be cut into
smaller pieces. This dramatically increases the complexity of the problem,
since each piece should be individually and manually pre-aligned. To the best
of our knowledge, no automatic method can reliably locate such piece of tissue
within its respective whole in the MRI slice, and align it without any prior
information. We propose here a novel automatic approach to the joint problem of
multimodal registration between histology and MRI, when only a fraction of
tissue is available from histology. The approach relies on the representation
of images using their level lines so as to reach contrast invariance. Shape
elements obtained via the extraction of bitangents are encoded in a
projective-invariant manner, which permits the identification of common pieces
of curves between two images. We evaluated the approach on human brain
histology and compared resulting alignments against manually annotated ground
truths. Considering the complexity of the brain folding patterns, preliminary
results are promising and suggest the use of characteristic and meaningful
shape elements for improved robustness and efficiency.Comment: Paper accepted at ICCV Workshop (Bio-Image Computing
Image Segmentation Using Weak Shape Priors
The problem of image segmentation is known to become particularly challenging
in the case of partial occlusion of the object(s) of interest, background
clutter, and the presence of strong noise. To overcome this problem, the
present paper introduces a novel approach segmentation through the use of
"weak" shape priors. Specifically, in the proposed method, an segmenting active
contour is constrained to converge to a configuration at which its geometric
parameters attain their empirical probability densities closely matching the
corresponding model densities that are learned based on training samples. It is
shown through numerical experiments that the proposed shape modeling can be
regarded as "weak" in the sense that it minimally influences the segmentation,
which is allowed to be dominated by data-related forces. On the other hand, the
priors provide sufficient constraints to regularize the convergence of
segmentation, while requiring substantially smaller training sets to yield less
biased results as compared to the case of PCA-based regularization methods. The
main advantages of the proposed technique over some existing alternatives is
demonstrated in a series of experiments.Comment: 27 pages, 8 figure
Image processing for plastic surgery planning
This thesis presents some image processing tools for plastic surgery planning. In particular,
it presents a novel method that combines local and global context in a probabilistic
relaxation framework to identify cephalometric landmarks used in Maxillofacial plastic
surgery. It also uses a method that utilises global and local symmetry to identify abnormalities
in CT frontal images of the human body. The proposed methodologies are
evaluated with the help of several clinical data supplied by collaborating plastic surgeons
Statistical Model of Shape Moments with Active Contour Evolution for Shape Detection and Segmentation
This paper describes a novel method for shape representation and robust image segmentation. The proposed method combines two well known methodologies, namely, statistical shape models and active contours implemented in level set framework. The shape detection is achieved by maximizing a posterior function that consists of a prior shape probability model and image likelihood function conditioned on shapes. The statistical shape model is built as a result of a learning process based on nonparametric probability estimation in a PCA reduced feature space formed by the Legendre moments of training silhouette images. A greedy strategy is applied to optimize the proposed cost function by iteratively evolving an implicit active contour in the image space and subsequent constrained optimization of the evolved shape in the reduced shape feature space. Experimental results presented in the paper demonstrate that the proposed method, contrary to many other active contour segmentation methods, is highly resilient to severe random and structural noise that could be present in the data
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
Geometric and photometric affine invariant image registration
This thesis aims to present a solution to the correspondence problem for the registration
of wide-baseline images taken from uncalibrated cameras. We propose an affine
invariant descriptor that combines the geometry and photometry of the scene to find
correspondences between both views. The geometric affine invariant component of the
descriptor is based on the affine arc-length metric, whereas the photometry is analysed
by invariant colour moments. A graph structure represents the spatial distribution of the
primitive features; i.e. nodes correspond to detected high-curvature points, whereas arcs
represent connectivities by extracted contours. After matching, we refine the search for
correspondences by using a maximum likelihood robust algorithm. We have evaluated
the system over synthetic and real data. The method is endemic to propagation of errors
introduced by approximations in the system.BAE SystemsSelex Sensors and Airborne System
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