113 research outputs found
Deep convolutional neural networks for segmenting 3D in vivo multiphoton images of vasculature in Alzheimer disease mouse models
The health and function of tissue rely on its vasculature network to provide
reliable blood perfusion. Volumetric imaging approaches, such as multiphoton
microscopy, are able to generate detailed 3D images of blood vessels that could
contribute to our understanding of the role of vascular structure in normal
physiology and in disease mechanisms. The segmentation of vessels, a core image
analysis problem, is a bottleneck that has prevented the systematic comparison
of 3D vascular architecture across experimental populations. We explored the
use of convolutional neural networks to segment 3D vessels within volumetric in
vivo images acquired by multiphoton microscopy. We evaluated different network
architectures and machine learning techniques in the context of this
segmentation problem. We show that our optimized convolutional neural network
architecture, which we call DeepVess, yielded a segmentation accuracy that was
better than both the current state-of-the-art and a trained human annotator,
while also being orders of magnitude faster. To explore the effects of aging
and Alzheimer's disease on capillaries, we applied DeepVess to 3D images of
cortical blood vessels in young and old mouse models of Alzheimer's disease and
wild type littermates. We found little difference in the distribution of
capillary diameter or tortuosity between these groups, but did note a decrease
in the number of longer capillary segments () in aged animals as
compared to young, in both wild type and Alzheimer's disease mouse models.Comment: 34 pages, 9 figure
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Design Optimization Strategy for Multifunctional 3D Printing
An optimization based design methodology for the additive manufacture of multifunctional parts (for example, a structure with embedded electronic/electrical systems and
associated conductive paths) is presented. This work introduces a coupled optimization strategy
where Topology Optimization (TO) is combined with an automated placement and routing
approach that enables determination of an efficient internal system configuration. This permits
the effect of the incorporation of the internal system on the structural response of the part to be
taken into account and therefore enables the overall optimization of the structure-system unit. An
example test case is included in the paper to evaluate the optimization strategy and demonstrate
the methods effectiveness. The capability of this method allows the exploitation of the
manufacturing capability under development within the Additive Manufacturing (AM)
community to produce 3D internal systems within complex structures.Mechanical Engineerin
Extraction of airway trees using multiple hypothesis tracking and template matching
Knowledge of airway tree morphology has important clinical applications in
diagnosis of chronic obstructive pulmonary disease. We present an automatic
tree extraction method based on multiple hypothesis tracking and template
matching for this purpose and evaluate its performance on chest CT images. The
method is adapted from a semi-automatic method devised for vessel segmentation.
Idealized tubular templates are constructed that match airway probability
obtained from a trained classifier and ranked based on their relative
significance. Several such regularly spaced templates form the local hypotheses
used in constructing a multiple hypothesis tree, which is then traversed to
reach decisions. The proposed modifications remove the need for local
thresholding of hypotheses as decisions are made entirely based on statistical
comparisons involving the hypothesis tree. The results show improvements in
performance when compared to the original method and region growing on
intensity images. We also compare the method with region growing on the
probability images, where the presented method does not show substantial
improvement, but we expect it to be less sensitive to local anomalies in the
data.Comment: 12 pages. Presented at the MICCAI Pulmonary Image Analysis Workshop,
Athens, Greece, 201
Extracting Tree-structures in CT data by Tracking Multiple Statistically Ranked Hypotheses
In this work, we adapt a method based on multiple hypothesis tracking (MHT)
that has been shown to give state-of-the-art vessel segmentation results in
interactive settings, for the purpose of extracting trees. Regularly spaced
tubular templates are fit to image data forming local hypotheses. These local
hypotheses are used to construct the MHT tree, which is then traversed to make
segmentation decisions. However, some critical parameters in this method are
scale-dependent and have an adverse effect when tracking structures of varying
dimensions. We propose to use statistical ranking of local hypotheses in
constructing the MHT tree, which yields a probabilistic interpretation of
scores across scales and helps alleviate the scale-dependence of MHT
parameters. This enables our method to track trees starting from a single seed
point. Our method is evaluated on chest CT data to extract airway trees and
coronary arteries. In both cases, we show that our method performs
significantly better than the original MHT method.Comment: Accepted for publication at the International Journal of Medical
Physics and Practic
Seeing Tree Structure from Vibration
Humans recognize object structure from both their appearance and motion;
often, motion helps to resolve ambiguities in object structure that arise when
we observe object appearance only. There are particular scenarios, however,
where neither appearance nor spatial-temporal motion signals are informative:
occluding twigs may look connected and have almost identical movements, though
they belong to different, possibly disconnected branches. We propose to tackle
this problem through spectrum analysis of motion signals, because vibrations of
disconnected branches, though visually similar, often have distinctive natural
frequencies. We propose a novel formulation of tree structure based on a
physics-based link model, and validate its effectiveness by theoretical
analysis, numerical simulation, and empirical experiments. With this
formulation, we use nonparametric Bayesian inference to reconstruct tree
structure from both spectral vibration signals and appearance cues. Our model
performs well in recognizing hierarchical tree structure from real-world videos
of trees and vessels.Comment: ECCV 2018. The first two authors contributed equally to this work.
Project page: http://tree.csail.mit.edu
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