3,959 research outputs found
EPiK-a Workflow for Electron Tomography in Kepler.
Scientific workflows integrate data and computing interfaces as configurable, semi-automatic graphs to solve a scientific problem. Kepler is such a software system for designing, executing, reusing, evolving, archiving and sharing scientific workflows. Electron tomography (ET) enables high-resolution views of complex cellular structures, such as cytoskeletons, organelles, viruses and chromosomes. Imaging investigations produce large datasets. For instance, in Electron Tomography, the size of a 16 fold image tilt series is about 65 Gigabytes with each projection image including 4096 by 4096 pixels. When we use serial sections or montage technique for large field ET, the dataset will be even larger. For higher resolution images with multiple tilt series, the data size may be in terabyte range. Demands of mass data processing and complex algorithms require the integration of diverse codes into flexible software structures. This paper describes a workflow for Electron Tomography Programs in Kepler (EPiK). This EPiK workflow embeds the tracking process of IMOD, and realizes the main algorithms including filtered backprojection (FBP) from TxBR and iterative reconstruction methods. We have tested the three dimensional (3D) reconstruction process using EPiK on ET data. EPiK can be a potential toolkit for biology researchers with the advantage of logical viewing, easy handling, convenient sharing and future extensibility
Parallel load balancing strategy for Volume-of-Fluid methods on 3-D unstructured meshes
© 2016. This version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/l Volume-of-Fluid (VOF) is one of the methods of choice to reproduce the interface motion in the simulation of multi-fluid flows. One of its main strengths is its accuracy in capturing sharp interface geometries, although requiring for it a number of geometric calculations. Under these circumstances, achieving parallel performance on current supercomputers is a must. The main obstacle for the parallelization is that the computing costs are concentrated only in the discrete elements that lie on the interface between fluids. Consequently, if the interface is not homogeneously distributed throughout the domain, standard domain decomposition (DD) strategies lead to imbalanced workload distributions. In this paper, we present a new parallelization strategy for general unstructured VOF solvers, based on a dynamic load balancing process complementary to the underlying DD. Its parallel efficiency has been analyzed and compared to the DD one using up to 1024 CPU-cores on an Intel SandyBridge based supercomputer. The results obtained on the solution of several artificially generated test cases show a speedup of up to similar to 12x with respect to the standard DD, depending on the interface size, the initial distribution and the number of parallel processes engaged. Moreover, the new parallelization strategy presented is of general purpose, therefore, it could be used to parallelize any VOF solver without requiring changes on the coupled flow solver. Finally, note that although designed for the VOF method, our approach could be easily adapted to other interface-capturing methods, such as the Level-Set, which may present similar workload imbalances. (C) 2014 Elsevier Inc. Allrights reserved.Peer ReviewedPostprint (author's final draft
A Real-time Image Reconstruction System for Particle Treatment Planning Using Proton Computed Tomography (pCT)
Proton computed tomography (pCT) is a novel medical imaging modality for
mapping the distribution of proton relative stopping power (RSP) in medical
objects of interest. Compared to conventional X-ray computed tomography, where
range uncertainty margins are around 3.5%, pCT has the potential to provide
more accurate measurements to within 1%. This improved efficiency will be
beneficial to proton-therapy planning and pre-treatment verification. A
prototype pCT imaging device has recently been developed capable of rapidly
acquiring low-dose proton radiographs of head-sized objects. We have also
developed an advanced, fast image reconstruction software based on distributed
computing that utilizes parallel processors and graphical processing units. The
combination of fast data acquisition and fast image reconstruction will enable
the availability of RSP images within minutes for use in clinical settings. The
performance of our image reconstruction software has been evaluated using data
collected by the prototype pCT scanner from several phantoms.Comment: Paper presented at Conference on the Application of Accelerators in
Research and Industry, CAARI 2016, 30 October to 4 November 2016, Ft. Worth,
TX, US
Efficient Inversion of Multiple-Scattering Model for Optical Diffraction Tomography
Optical diffraction tomography relies on solving an inverse scattering
problem governed by the wave equation. Classical reconstruction algorithms are
based on linear approximations of the forward model (Born or Rytov), which
limits their applicability to thin samples with low refractive-index contrasts.
More recent works have shown the benefit of adopting nonlinear models. They
account for multiple scattering and reflections, improving the quality of
reconstruction. To reduce the complexity and memory requirements of these
methods, we derive an explicit formula for the Jacobian matrix of the nonlinear
Lippmann-Schwinger model which lends itself to an efficient evaluation of the
gradient of the data- fidelity term. This allows us to deploy efficient methods
to solve the corresponding inverse problem subject to sparsity constraints
Applications in GNSS water vapor tomography
Algebraic reconstruction algorithms are iterative algorithms that are used in many area including medicine, seismology or meteorology. These algorithms are known to be highly computational intensive. This may be especially troublesome for real-time applications or when processed by conventional low-cost personnel computers. One of these real time applications
is the reconstruction of water vapor images from Global Navigation Satellite System (GNSS) observations. The parallelization of algebraic reconstruction algorithms has the potential to diminish signi cantly the required resources permitting to obtain valid solutions in time to be used for nowcasting and forecasting weather models.
The main objective of this dissertation was to present and analyse diverse shared memory
libraries and techniques in CPU and GPU for algebraic reconstruction algorithms. It was concluded that the parallelization compensates over sequential implementations. Overall the GPU implementations were found to be only slightly faster than the CPU implementations, depending on the size of the problem being studied.
A secondary objective was to develop a software to perform the GNSS water vapor reconstruction using the implemented parallel algorithms. This software has been developed with success and diverse tests were made namely with synthetic and real data, the preliminary results shown to be satisfactory.
This dissertation was written in the Space & Earth Geodetic Analysis Laboratory (SEGAL) and was carried out in the framework of the Structure of Moist convection in high-resolution GNSS observations and models (SMOG) (PTDC/CTE-ATM/119922/2010) project funded by FCT.Algoritmos de reconstrução algébrica são algoritmos iterativos que são usados em muitas áreas
incluindo medicina, sismologia ou meteorologia. Estes algoritmos são conhecidos por serem bastante
exigentes computacionalmente. Isto pode ser especialmente complicado para aplicações
de tempo real ou quando processados por computadores pessoais de baixo custo. Uma destas
aplicações de tempo real é a reconstrução de imagens de vapor de água a partir de observações
de sistemas globais de navegação por satélite. A paralelização dos algoritmos de reconstrução
algébrica permite que se reduza significativamente os requisitos computacionais permitindo
obter soluções válidas para previsão meteorológica num curto espaço de tempo.
O principal objectivo desta dissertação é apresentar e analisar diversas bibliotecas e técnicas
multithreading para a reconstrução algébrica em CPU e GPU. Foi concluído que a paralelização
compensa sobre a implementações sequenciais. De um modo geral as implementações GPU
obtiveram resultados relativamente melhores que implementações em CPU, isto dependendo do
tamanho do problema a ser estudado. Um objectivo secundário era desenvolver uma aplicação
que realizasse a reconstrução de imagem de vapor de água através de sistemas globais de
navegação por satélite de uma forma paralela. Este software tem sido desenvolvido com sucesso
e diversos testes foram realizados com dados sintéticos e dados reais, os resultados preliminares
foram satisfatórios.
Esta dissertação foi escrita no Space & Earth Geodetic Analysis Laboratory (SEGAL) e foi realizada de acordo com o projecto Structure 01' Moist convection in high-resolution GNSS observations and models (SMOG) (PTDC / CTE-ATM/ 11992212010) financiado pelo FCT.Fundação para a Ciência e a Tecnologia (FCT
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
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