9,656 research outputs found
Algorithms to automatically quantify the geometric similarity of anatomical surfaces
We describe new approaches for distances between pairs of 2-dimensional
surfaces (embedded in 3-dimensional space) that use local structures and global
information contained in inter-structure geometric relationships. We present
algorithms to automatically determine these distances as well as geometric
correspondences. This is motivated by the aspiration of students of natural
science to understand the continuity of form that unites the diversity of life.
At present, scientists using physical traits to study evolutionary
relationships among living and extinct animals analyze data extracted from
carefully defined anatomical correspondence points (landmarks). Identifying and
recording these landmarks is time consuming and can be done accurately only by
trained morphologists. This renders these studies inaccessible to
non-morphologists, and causes phenomics to lag behind genomics in elucidating
evolutionary patterns. Unlike other algorithms presented for morphological
correspondences our approach does not require any preliminary marking of
special features or landmarks by the user. It also differs from other seminal
work in computational geometry in that our algorithms are polynomial in nature
and thus faster, making pairwise comparisons feasible for significantly larger
numbers of digitized surfaces. We illustrate our approach using three datasets
representing teeth and different bones of primates and humans, and show that it
leads to highly accurate results.Comment: Changes with respect to v1, v2: an Erratum was added, correcting the
references for one of the three datasets. Note that the datasets and code for
this paper can be obtained from the Data Conservancy (see Download column on
v1, v2
Deep learning cardiac motion analysis for human survival prediction
Motion analysis is used in computer vision to understand the behaviour of
moving objects in sequences of images. Optimising the interpretation of dynamic
biological systems requires accurate and precise motion tracking as well as
efficient representations of high-dimensional motion trajectories so that these
can be used for prediction tasks. Here we use image sequences of the heart,
acquired using cardiac magnetic resonance imaging, to create time-resolved
three-dimensional segmentations using a fully convolutional network trained on
anatomical shape priors. This dense motion model formed the input to a
supervised denoising autoencoder (4Dsurvival), which is a hybrid network
consisting of an autoencoder that learns a task-specific latent code
representation trained on observed outcome data, yielding a latent
representation optimised for survival prediction. To handle right-censored
survival outcomes, our network used a Cox partial likelihood loss function. In
a study of 302 patients the predictive accuracy (quantified by Harrell's
C-index) was significantly higher (p < .0001) for our model C=0.73 (95 CI:
0.68 - 0.78) than the human benchmark of C=0.59 (95 CI: 0.53 - 0.65). This
work demonstrates how a complex computer vision task using high-dimensional
medical image data can efficiently predict human survival
3D Model Assisted Image Segmentation
The problem of segmenting a given image into coherent regions is important in Computer Vision and many industrial applications require segmenting a known object into its components. Examples include identifying individual parts of a component for proces
GOGMA: Globally-Optimal Gaussian Mixture Alignment
Gaussian mixture alignment is a family of approaches that are frequently used
for robustly solving the point-set registration problem. However, since they
use local optimisation, they are susceptible to local minima and can only
guarantee local optimality. Consequently, their accuracy is strongly dependent
on the quality of the initialisation. This paper presents the first
globally-optimal solution to the 3D rigid Gaussian mixture alignment problem
under the L2 distance between mixtures. The algorithm, named GOGMA, employs a
branch-and-bound approach to search the space of 3D rigid motions SE(3),
guaranteeing global optimality regardless of the initialisation. The geometry
of SE(3) was used to find novel upper and lower bounds for the objective
function and local optimisation was integrated into the scheme to accelerate
convergence without voiding the optimality guarantee. The evaluation
empirically supported the optimality proof and showed that the method performed
much more robustly on two challenging datasets than an existing
globally-optimal registration solution.Comment: Manuscript in press 2016 IEEE Conference on Computer Vision and
Pattern Recognitio
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