13,311 research outputs found
Robust semi-automated path extraction for visualising stenosis of the coronary arteries
Computed tomography angiography (CTA) is useful for diagnosing and planning treatment of heart disease. However, contrast agent in surrounding structures (such as the aorta and left ventricle) makes 3-D visualisation of the coronary arteries difficult. This paper presents a composite method employing segmentation and volume rendering to overcome this issue. A key contribution is a novel Fast Marching minimal path cost function for vessel centreline extraction. The resultant centreline is used to compute a measure of vessel lumen, which indicates the degree of stenosis (narrowing of a vessel). Two volume visualisation techniques are presented which utilise the segmented arteries and lumen measure. The system is evaluated and demonstrated using synthetic and clinically obtained datasets
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
Integration of multimodal data based on surface registration
The paper proposes and evaluates a strategy for the alignment of
anatomical and functional data of the brain. The method takes as an
input two different sets of images of a same patient: MR data and
SPECT. It proceeds in four steps: first, it constructs two voxel
models from the two image sets; next, it extracts from the two voxel
models the surfaces of regions of interest; in the third step, the
surfaces are interactively aligned by corresponding pairs; finally a
unique volume model is constructed by selectively applying the
geometrical transformations associated to the regions and weighting
their contributions. The main advantages of this strategy are (i) that
it can be applied retrospectively, (ii) that it is tri-dimensional,
and (iii) that it is local. Its main disadvantage with regard to
previously published methods it that it requires the extraction of
surfaces. However, this step is often required for other stages of the
multimodal analysis such as the visualization and therefore its cost
can be accounted in the global cost of the process.Postprint (published version
Unwind: Interactive Fish Straightening
The ScanAllFish project is a large-scale effort to scan all the world's
33,100 known species of fishes. It has already generated thousands of
volumetric CT scans of fish species which are available on open access
platforms such as the Open Science Framework. To achieve a scanning rate
required for a project of this magnitude, many specimens are grouped together
into a single tube and scanned all at once. The resulting data contain many
fish which are often bent and twisted to fit into the scanner. Our system,
Unwind, is a novel interactive visualization and processing tool which
extracts, unbends, and untwists volumetric images of fish with minimal user
interaction. Our approach enables scientists to interactively unwarp these
volumes to remove the undesired torque and bending using a piecewise-linear
skeleton extracted by averaging isosurfaces of a harmonic function connecting
the head and tail of each fish. The result is a volumetric dataset of a
individual, straight fish in a canonical pose defined by the marine biologist
expert user. We have developed Unwind in collaboration with a team of marine
biologists: Our system has been deployed in their labs, and is presently being
used for dataset construction, biomechanical analysis, and the generation of
figures for scientific publication
SurfelMeshing: Online Surfel-Based Mesh Reconstruction
We address the problem of mesh reconstruction from live RGB-D video, assuming
a calibrated camera and poses provided externally (e.g., by a SLAM system). In
contrast to most existing approaches, we do not fuse depth measurements in a
volume but in a dense surfel cloud. We asynchronously (re)triangulate the
smoothed surfels to reconstruct a surface mesh. This novel approach enables to
maintain a dense surface representation of the scene during SLAM which can
quickly adapt to loop closures. This is possible by deforming the surfel cloud
and asynchronously remeshing the surface where necessary. The surfel-based
representation also naturally supports strongly varying scan resolution. In
particular, it reconstructs colors at the input camera's resolution. Moreover,
in contrast to many volumetric approaches, ours can reconstruct thin objects
since objects do not need to enclose a volume. We demonstrate our approach in a
number of experiments, showing that it produces reconstructions that are
competitive with the state-of-the-art, and we discuss its advantages and
limitations. The algorithm (excluding loop closure functionality) is available
as open source at https://github.com/puzzlepaint/surfelmeshing .Comment: Version accepted to IEEE Transactions on Pattern Analysis and Machine
Intelligenc
Fast connected component labeling algorithm: a non voxel-based approach
This paper presents a new approach to achieve connected component labeling on both binary images and volumes by using the Extreme Vertices Model (EVM), a representation model for orthogonal
polyhedra, applied to digital images and volume datasets recently. In contrast with previous techniques, this method does not use a voxel-based approach but deals with the inner sections of the object.Postprint (published version
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