6,825 research outputs found
Template-Cut: A Pattern-Based Segmentation Paradigm
We present a scale-invariant, template-based segmentation paradigm that sets
up a graph and performs a graph cut to separate an object from the background.
Typically graph-based schemes distribute the nodes of the graph uniformly and
equidistantly on the image, and use a regularizer to bias the cut towards a
particular shape. The strategy of uniform and equidistant nodes does not allow
the cut to prefer more complex structures, especially when areas of the object
are indistinguishable from the background. We propose a solution by introducing
the concept of a "template shape" of the target object in which the nodes are
sampled non-uniformly and non-equidistantly on the image. We evaluate it on
2D-images where the object's textures and backgrounds are similar, and large
areas of the object have the same gray level appearance as the background. We
also evaluate it in 3D on 60 brain tumor datasets for neurosurgical planning
purposes.Comment: 8 pages, 6 figures, 3 tables, 6 equations, 51 reference
Visual Quality Enhancement in Optoacoustic Tomography using Active Contour Segmentation Priors
Segmentation of biomedical images is essential for studying and
characterizing anatomical structures, detection and evaluation of pathological
tissues. Segmentation has been further shown to enhance the reconstruction
performance in many tomographic imaging modalities by accounting for
heterogeneities of the excitation field and tissue properties in the imaged
region. This is particularly relevant in optoacoustic tomography, where
discontinuities in the optical and acoustic tissue properties, if not properly
accounted for, may result in deterioration of the imaging performance.
Efficient segmentation of optoacoustic images is often hampered by the
relatively low intrinsic contrast of large anatomical structures, which is
further impaired by the limited angular coverage of some commonly employed
tomographic imaging configurations. Herein, we analyze the performance of
active contour models for boundary segmentation in cross-sectional optoacoustic
tomography. The segmented mask is employed to construct a two compartment model
for the acoustic and optical parameters of the imaged tissues, which is
subsequently used to improve accuracy of the image reconstruction routines. The
performance of the suggested segmentation and modeling approach are showcased
in tissue-mimicking phantoms and small animal imaging experiments.Comment: Accepted for publication in IEEE Transactions on Medical Imagin
A workflow for the automatic segmentation of organelles in electron microscopy image stacks.
Electron microscopy (EM) facilitates analysis of the form, distribution, and functional status of key organelle systems in various pathological processes, including those associated with neurodegenerative disease. Such EM data often provide important new insights into the underlying disease mechanisms. The development of more accurate and efficient methods to quantify changes in subcellular microanatomy has already proven key to understanding the pathogenesis of Parkinson's and Alzheimer's diseases, as well as glaucoma. While our ability to acquire large volumes of 3D EM data is progressing rapidly, more advanced analysis tools are needed to assist in measuring precise three-dimensional morphologies of organelles within data sets that can include hundreds to thousands of whole cells. Although new imaging instrument throughputs can exceed teravoxels of data per day, image segmentation and analysis remain significant bottlenecks to achieving quantitative descriptions of whole cell structural organellomes. Here, we present a novel method for the automatic segmentation of organelles in 3D EM image stacks. Segmentations are generated using only 2D image information, making the method suitable for anisotropic imaging techniques such as serial block-face scanning electron microscopy (SBEM). Additionally, no assumptions about 3D organelle morphology are made, ensuring the method can be easily expanded to any number of structurally and functionally diverse organelles. Following the presentation of our algorithm, we validate its performance by assessing the segmentation accuracy of different organelle targets in an example SBEM dataset and demonstrate that it can be efficiently parallelized on supercomputing resources, resulting in a dramatic reduction in runtime
A Combinatorial Solution to Non-Rigid 3D Shape-to-Image Matching
We propose a combinatorial solution for the problem of non-rigidly matching a
3D shape to 3D image data. To this end, we model the shape as a triangular mesh
and allow each triangle of this mesh to be rigidly transformed to achieve a
suitable matching to the image. By penalising the distance and the relative
rotation between neighbouring triangles our matching compromises between image
and shape information. In this paper, we resolve two major challenges: Firstly,
we address the resulting large and NP-hard combinatorial problem with a
suitable graph-theoretic approach. Secondly, we propose an efficient
discretisation of the unbounded 6-dimensional Lie group SE(3). To our knowledge
this is the first combinatorial formulation for non-rigid 3D shape-to-image
matching. In contrast to existing local (gradient descent) optimisation
methods, we obtain solutions that do not require a good initialisation and that
are within a bound of the optimal solution. We evaluate the proposed method on
the two problems of non-rigid 3D shape-to-shape and non-rigid 3D shape-to-image
registration and demonstrate that it provides promising results.Comment: 10 pages, 7 figure
Cube-Cut: Vertebral Body Segmentation in MRI-Data through Cubic-Shaped Divergences
In this article, we present a graph-based method using a cubic template for
volumetric segmentation of vertebrae in magnetic resonance imaging (MRI)
acquisitions. The user can define the degree of deviation from a regular cube
via a smoothness value Delta. The Cube-Cut algorithm generates a directed graph
with two terminal nodes (s-t-network), where the nodes of the graph correspond
to a cubic-shaped subset of the image's voxels. The weightings of the graph's
terminal edges, which connect every node with a virtual source s or a virtual
sink t, represent the affinity of a voxel to the vertebra (source) and to the
background (sink). Furthermore, a set of infinite weighted and non-terminal
edges implements the smoothness term. After graph construction, a minimal
s-t-cut is calculated within polynomial computation time, which splits the
nodes into two disjoint units. Subsequently, the segmentation result is
determined out of the source-set. A quantitative evaluation of a C++
implementation of the algorithm resulted in an average Dice Similarity
Coefficient (DSC) of 81.33% and a running time of less than a minute.Comment: 23 figures, 2 tables, 43 references, PLoS ONE 9(4): e9338
A Pipeline for Volume Electron Microscopy of the Caenorhabditis elegans Nervous System.
The "connectome," a comprehensive wiring diagram of synaptic connectivity, is achieved through volume electron microscopy (vEM) analysis of an entire nervous system and all associated non-neuronal tissues. White et al. (1986) pioneered the fully manual reconstruction of a connectome using Caenorhabditis elegans. Recent advances in vEM allow mapping new C. elegans connectomes with increased throughput, and reduced subjectivity. Current vEM studies aim to not only fill the remaining gaps in the original connectome, but also address fundamental questions including how the connectome changes during development, the nature of individuality, sexual dimorphism, and how genetic and environmental factors regulate connectivity. Here we describe our current vEM pipeline and projected improvements for the study of the C. elegans nervous system and beyond
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