17,531 research outputs found
BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images
In cryo-electron microscopy (EM), molecular structures are determined from
large numbers of projection images of individual particles. To harness the full
power of this single-molecule information, we use the Bayesian inference of EM
(BioEM) formalism. By ranking structural models using posterior probabilities
calculated for individual images, BioEM in principle addresses the challenge of
working with highly dynamic or heterogeneous systems not easily handled in
traditional EM reconstruction. However, the calculation of these posteriors for
large numbers of particles and models is computationally demanding. Here we
present highly parallelized, GPU-accelerated computer software that performs
this task efficiently. Our flexible formulation employs CUDA, OpenMP, and MPI
parallelization combined with both CPU and GPU computing. The resulting BioEM
software scales nearly ideally both on pure CPU and on CPU+GPU architectures,
thus enabling Bayesian analysis of tens of thousands of images in a reasonable
time. The general mathematical framework and robust algorithms are not limited
to cryo-electron microscopy but can be generalized for electron tomography and
other imaging experiments
GPU-based Iterative Cone Beam CT Reconstruction Using Tight Frame Regularization
X-ray imaging dose from serial cone-beam CT (CBCT) scans raises a clinical
concern in most image guided radiation therapy procedures. It is the goal of
this paper to develop a fast GPU-based algorithm to reconstruct high quality
CBCT images from undersampled and noisy projection data so as to lower the
imaging dose. For this purpose, we have developed an iterative tight frame (TF)
based CBCT reconstruction algorithm. A condition that a real CBCT image has a
sparse representation under a TF basis is imposed in the iteration process as
regularization to the solution. To speed up the computation, a multi-grid
method is employed. Our GPU implementation has achieved high computational
efficiency and a CBCT image of resolution 512\times512\times70 can be
reconstructed in ~5 min. We have tested our algorithm on a digital NCAT phantom
and a physical Catphan phantom. It is found that our TF-based algorithm is able
to reconstrct CBCT in the context of undersampling and low mAs levels. We have
also quantitatively analyzed the reconstructed CBCT image quality in terms of
modulation-transfer-function and contrast-to-noise ratio under various scanning
conditions. The results confirm the high CBCT image quality obtained from our
TF algorithm. Moreover, our algorithm has also been validated in a real
clinical context using a head-and-neck patient case. Comparisons of the
developed TF algorithm and the current state-of-the-art TV algorithm have also
been made in various cases studied in terms of reconstructed image quality and
computation efficiency.Comment: 24 pages, 8 figures, accepted by Phys. Med. Bio
Acceleration of stereo-matching on multi-core CPU and GPU
This paper presents an accelerated version of a
dense stereo-correspondence algorithm for two different parallelism
enabled architectures, multi-core CPU and GPU. The
algorithm is part of the vision system developed for a binocular
robot-head in the context of the CloPeMa 1 research project.
This research project focuses on the conception of a new clothes
folding robot with real-time and high resolution requirements
for the vision system. The performance analysis shows that
the parallelised stereo-matching algorithm has been significantly
accelerated, maintaining 12x and 176x speed-up respectively
for multi-core CPU and GPU, compared with non-SIMD singlethread
CPU. To analyse the origin of the speed-up and gain
deeper understanding about the choice of the optimal hardware,
the algorithm was broken into key sub-tasks and the performance
was tested for four different hardware architectures
Learning Deep CNN Denoiser Prior for Image Restoration
Model-based optimization methods and discriminative learning methods have
been the two dominant strategies for solving various inverse problems in
low-level vision. Typically, those two kinds of methods have their respective
merits and drawbacks, e.g., model-based optimization methods are flexible for
handling different inverse problems but are usually time-consuming with
sophisticated priors for the purpose of good performance; in the meanwhile,
discriminative learning methods have fast testing speed but their application
range is greatly restricted by the specialized task. Recent works have revealed
that, with the aid of variable splitting techniques, denoiser prior can be
plugged in as a modular part of model-based optimization methods to solve other
inverse problems (e.g., deblurring). Such an integration induces considerable
advantage when the denoiser is obtained via discriminative learning. However,
the study of integration with fast discriminative denoiser prior is still
lacking. To this end, this paper aims to train a set of fast and effective CNN
(convolutional neural network) denoisers and integrate them into model-based
optimization method to solve other inverse problems. Experimental results
demonstrate that the learned set of denoisers not only achieve promising
Gaussian denoising results but also can be used as prior to deliver good
performance for various low-level vision applications.Comment: Accepted to CVPR 2017. Code: https://github.com/cszn/ircn
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