96,579 research outputs found
Knowing what you know in brain segmentation using Bayesian deep neural networks
In this paper, we describe a Bayesian deep neural network (DNN) for
predicting FreeSurfer segmentations of structural MRI volumes, in minutes
rather than hours. The network was trained and evaluated on a large dataset (n
= 11,480), obtained by combining data from more than a hundred different sites,
and also evaluated on another completely held-out dataset (n = 418). The
network was trained using a novel spike-and-slab dropout-based variational
inference approach. We show that, on these datasets, the proposed Bayesian DNN
outperforms previously proposed methods, in terms of the similarity between the
segmentation predictions and the FreeSurfer labels, and the usefulness of the
estimate uncertainty of these predictions. In particular, we demonstrated that
the prediction uncertainty of this network at each voxel is a good indicator of
whether the network has made an error and that the uncertainty across the whole
brain can predict the manual quality control ratings of a scan. The proposed
Bayesian DNN method should be applicable to any new network architecture for
addressing the segmentation problem.Comment: Submitted to Frontiers in Neuroinformatic
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
Manual-protocol inspired technique for improving automated MR image segmentation during label fusion
Recent advances in multi-atlas based algorithms address many of the previous limitations in model-based and probabilistic segmentation methods. However, at the label fusion stage, a majority of algorithms focus primarily on optimizing weight-maps associated with the atlas library based on a theoretical objective function that approximates the segmentation error. In contrast, we propose a novel method-Autocorrecting Walks over Localized Markov Random Fields (AWoL-MRF)-that aims at mimicking the sequential process of manual segmentation, which is the gold-standard for virtually all the segmentation methods. AWoL-MRF begins with a set of candidate labels generated by a multi-atlas segmentation pipeline as an initial label distribution and refines low confidence regions based on a localized Markov random field (L-MRF) model using a novel sequential inference process (walks). We show that AWoL-MRF produces state-of-the-art results with superior accuracy and robustness with a small atlas library compared to existing methods. We validate the proposed approach by performing hippocampal segmentations on three independent datasets: (1) Alzheimer\u27s Disease Neuroimaging Database (ADNI); (2) First Episode Psychosis patient cohort; and (3) A cohort of preterm neonates scanned early in life and at term-equivalent age. We assess the improvement in the performance qualitatively as well as quantitatively by comparing AWoL-MRF with majority vote, STAPLE, and Joint Label Fusion methods. AWoL-MRF reaches a maximum accuracy of 0.881 (dataset 1), 0.897 (dataset 2), and 0.807 (dataset 3) based on Dice similarity coefficient metric, offering significant performance improvements with a smaller atlas library (\u3c 10) over compared methods. We also evaluate the diagnostic utility of AWoL-MRF by analyzing the volume differences per disease category in the ADNI1: Complete Screening dataset. We have made the source code for AWoL-MRF public at: https://github.com/CobraLab/AWoL-MRF
MHP-VOS: Multiple Hypotheses Propagation for Video Object Segmentation
We address the problem of semi-supervised video object segmentation (VOS),
where the masks of objects of interests are given in the first frame of an
input video. To deal with challenging cases where objects are occluded or
missing, previous work relies on greedy data association strategies that make
decisions for each frame individually. In this paper, we propose a novel
approach to defer the decision making for a target object in each frame, until
a global view can be established with the entire video being taken into
consideration. Our approach is in the same spirit as Multiple Hypotheses
Tracking (MHT) methods, making several critical adaptations for the VOS
problem. We employ the bounding box (bbox) hypothesis for tracking tree
formation, and the multiple hypotheses are spawned by propagating the preceding
bbox into the detected bbox proposals within a gated region starting from the
initial object mask in the first frame. The gated region is determined by a
gating scheme which takes into account a more comprehensive motion model rather
than the simple Kalman filtering model in traditional MHT. To further design
more customized algorithms tailored for VOS, we develop a novel mask
propagation score instead of the appearance similarity score that could be
brittle due to large deformations. The mask propagation score, together with
the motion score, determines the affinity between the hypotheses during tree
pruning. Finally, a novel mask merging strategy is employed to handle mask
conflicts between objects. Extensive experiments on challenging datasets
demonstrate the effectiveness of the proposed method, especially in the case of
object missing.Comment: accepted to CVPR 2019 as oral presentatio
Backtracking Spatial Pyramid Pooling (SPP)-based Image Classifier for Weakly Supervised Top-down Salient Object Detection
Top-down saliency models produce a probability map that peaks at target
locations specified by a task/goal such as object detection. They are usually
trained in a fully supervised setting involving pixel-level annotations of
objects. We propose a weakly supervised top-down saliency framework using only
binary labels that indicate the presence/absence of an object in an image.
First, the probabilistic contribution of each image region to the confidence of
a CNN-based image classifier is computed through a backtracking strategy to
produce top-down saliency. From a set of saliency maps of an image produced by
fast bottom-up saliency approaches, we select the best saliency map suitable
for the top-down task. The selected bottom-up saliency map is combined with the
top-down saliency map. Features having high combined saliency are used to train
a linear SVM classifier to estimate feature saliency. This is integrated with
combined saliency and further refined through a multi-scale
superpixel-averaging of saliency map. We evaluate the performance of the
proposed weakly supervised topdown saliency and achieve comparable performance
with fully supervised approaches. Experiments are carried out on seven
challenging datasets and quantitative results are compared with 40 closely
related approaches across 4 different applications.Comment: 14 pages, 7 figure
Planar Ultrametric Rounding for Image Segmentation
We study the problem of hierarchical clustering on planar graphs. We
formulate this in terms of an LP relaxation of ultrametric rounding. To solve
this LP efficiently we introduce a dual cutting plane scheme that uses minimum
cost perfect matching as a subroutine in order to efficiently explore the space
of planar partitions. We apply our algorithm to the problem of hierarchical
image segmentation
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