1,278 research outputs found
Efficient Irregular Wavefront Propagation Algorithms on Hybrid CPU-GPU Machines
In this paper, we address the problem of efficient execution of a computation
pattern, referred to here as the irregular wavefront propagation pattern
(IWPP), on hybrid systems with multiple CPUs and GPUs. The IWPP is common in
several image processing operations. In the IWPP, data elements in the
wavefront propagate waves to their neighboring elements on a grid if a
propagation condition is satisfied. Elements receiving the propagated waves
become part of the wavefront. This pattern results in irregular data accesses
and computations. We develop and evaluate strategies for efficient computation
and propagation of wavefronts using a multi-level queue structure. This queue
structure improves the utilization of fast memories in a GPU and reduces
synchronization overheads. We also develop a tile-based parallelization
strategy to support execution on multiple CPUs and GPUs. We evaluate our
approaches on a state-of-the-art GPU accelerated machine (equipped with 3 GPUs
and 2 multicore CPUs) using the IWPP implementations of two widely used image
processing operations: morphological reconstruction and euclidean distance
transform. Our results show significant performance improvements on GPUs. The
use of multiple CPUs and GPUs cooperatively attains speedups of 50x and 85x
with respect to single core CPU executions for morphological reconstruction and
euclidean distance transform, respectively.Comment: 37 pages, 16 figure
Automated Segmentation of Pulmonary Lobes using Coordination-Guided Deep Neural Networks
The identification of pulmonary lobes is of great importance in disease
diagnosis and treatment. A few lung diseases have regional disorders at lobar
level. Thus, an accurate segmentation of pulmonary lobes is necessary. In this
work, we propose an automated segmentation of pulmonary lobes using
coordination-guided deep neural networks from chest CT images. We first employ
an automated lung segmentation to extract the lung area from CT image, then
exploit volumetric convolutional neural network (V-net) for segmenting the
pulmonary lobes. To reduce the misclassification of different lobes, we
therefore adopt coordination-guided convolutional layers (CoordConvs) that
generate additional feature maps of the positional information of pulmonary
lobes. The proposed model is trained and evaluated on a few publicly available
datasets and has achieved the state-of-the-art accuracy with a mean Dice
coefficient index of 0.947 0.044.Comment: ISBI 2019 (Oral
TernausNetV2: Fully Convolutional Network for Instance Segmentation
The most common approaches to instance segmentation are complex and use
two-stage networks with object proposals, conditional random-fields, template
matching or recurrent neural networks. In this work we present TernausNetV2 - a
simple fully convolutional network that allows extracting objects from a
high-resolution satellite imagery on an instance level. The network has popular
encoder-decoder type of architecture with skip connections but has a few
essential modifications that allows using for semantic as well as for instance
segmentation tasks. This approach is universal and allows to extend any network
that has been successfully applied for semantic segmentation to perform
instance segmentation task. In addition, we generalize network encoder that was
pre-trained for RGB images to use additional input channels. It makes possible
to use transfer learning from visual to a wider spectral range. For
DeepGlobe-CVPR 2018 building detection sub-challenge, based on public
leaderboard score, our approach shows superior performance in comparison to
other methods. The source code corresponding pre-trained weights are publicly
available at https://github.com/ternaus/TernausNetV
AxonDeepSeg: automatic axon and myelin segmentation from microscopy data using convolutional neural networks
Segmentation of axon and myelin from microscopy images of the nervous system
provides useful quantitative information about the tissue microstructure, such
as axon density and myelin thickness. This could be used for instance to
document cell morphometry across species, or to validate novel non-invasive
quantitative magnetic resonance imaging techniques. Most currently-available
segmentation algorithms are based on standard image processing and usually
require multiple processing steps and/or parameter tuning by the user to adapt
to different modalities. Moreover, only few methods are publicly available. We
introduce AxonDeepSeg, an open-source software that performs axon and myelin
segmentation of microscopic images using deep learning. AxonDeepSeg features:
(i) a convolutional neural network architecture; (ii) an easy training
procedure to generate new models based on manually-labelled data and (iii) two
ready-to-use models trained from scanning electron microscopy (SEM) and
transmission electron microscopy (TEM). Results show high pixel-wise accuracy
across various species: 85% on rat SEM, 81% on human SEM, 95% on mice TEM and
84% on macaque TEM. Segmentation of a full rat spinal cord slice is computed
and morphological metrics are extracted and compared against the literature.
AxonDeepSeg is freely available at https://github.com/neuropoly/axondeepsegComment: 14 pages, 7 figure
Spinal cord gray matter segmentation using deep dilated convolutions
Gray matter (GM) tissue changes have been associated with a wide range of
neurological disorders and was also recently found relevant as a biomarker for
disability in amyotrophic lateral sclerosis. The ability to automatically
segment the GM is, therefore, an important task for modern studies of the
spinal cord. In this work, we devise a modern, simple and end-to-end fully
automated human spinal cord gray matter segmentation method using Deep
Learning, that works both on in vivo and ex vivo MRI acquisitions. We evaluate
our method against six independently developed methods on a GM segmentation
challenge and report state-of-the-art results in 8 out of 10 different
evaluation metrics as well as major network parameter reduction when compared
to the traditional medical imaging architectures such as U-Nets.Comment: 13 pages, 8 figure
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