Wrocław, Poland
Wrocław, Poland

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Tarnawski W.,Wroclaw University of Technology | Tarnawski W.,Vratis Ltd. | Kurtcuoglu V.,University of Zürich | Lorek P.,Wrocław University | And 7 more authors.
IEEE Journal of Biomedical and Health Informatics | Year: 2013

We present herein a robust algorithm for cell tracking in a sequence of time-lapse 2-D fluorescent microscopy images. Tracking is performed automatically via a multiphase active contours algorithm adapted to the segmentation of clustered nuclei with obscure boundaries. An ellipse fitting method is applied to avoid problems typically associated with clustered, overlapping, or dying cells, and to obtain more accurate segmentation and tracking results. We provide quantitative validation of results obtained with this new algorithm by comparing them to the results obtained from the established CellProfiler, MTrack2 (plugin for Fiji), and LSetCellTracker software. © 2013 IEEE.

Tomczak T.,Wroclaw University of Technology | Zadarnowska K.,Wroclaw University of Technology | Koza Z.,Wrocław University | Matyka M.,Wrocław University | And 2 more authors.
International Journal of Computational Fluid Dynamics | Year: 2013

While new power-efficient computer architectures exhibit spectacular theoretical peak performance, they require specific conditions to operate efficiently, which makes porting complex algorithms a challenge. Here, we report results of the semi-implicit method for pressure linked equations (SIMPLE) and the pressure implicit with operator splitting (PISO) methods implemented on the graphics processing unit (GPU). We examine the advantages and disadvantages of the full porting over a partial acceleration of these algorithms run on unstructured meshes. We found that the full-port strategy requires adjusting the internal data structures to the new hardware and proposed a convenient format for storing internal data structures on GPUs. Our implementation is validated on standard steady and unsteady problems and its computational efficiency is checked by comparing its results and run times with those of some standard software (OpenFOAM) run on central processing unit (CPU). The results show that a server-class GPU outperforms a server-class dual-socket multi-core CPU system running essentially the same algorithm by up to a factor of 4. © 2013 Copyright Taylor and Francis Group, LLC.

Matyka M.,Wrocław University | Koza Z.,Wrocław University | Miroslaw L.,Wroclaw University of Technology | Miroslaw L.,Vratis Ltd.
Computers and Fluids | Year: 2013

The wall shear stress is a quantity of profound importance for clinical diagnosis of artery diseases. The lattice Boltzmann is an easily parallelizable numerical method of solving the flow problems, but it suffers from errors of the wall shear stress near a non-smooth wall. In this work we present a simple formula to calculate the wall shear stress in the lattice Boltzmann model and propose to compute wall normals, which are necessary to compute the wall shear stress, by taking the weighted mean over boundary facets lying in a vicinity of a wall element. We carry out several tests and observe an increase of accuracy of computed normal vectors over other methods in two and three dimensions. Using the scheme we compute the wall shear stress in an inclined and bent channel fluid flow and show a minor influence of the normal on the numerical error, implying that the main error arises because the velocity vectors near the wall follow the shape of the staircase. Finally, we calculate the wall shear stress in the human abdominal aorta in steady conditions using our method and compare the results with a standard finite volume solver and experimental data available in the literature. Applications of our ideas in a simplified protocol for data preprocessing in medical applications are discussed. © 2013 Elsevier Ltd.

Greathouset J.L.,AMD Inc | Knoxt K.,AMD Inc | Pola J.,Wrocław University | Pola J.,Vratis Ltd. | And 2 more authors.
ACM International Conference Proceeding Series | Year: 2016

Sparse linear algebra is a cornerstone of modern computational science. These algorithms ignore the zero-valued entries found in many domains in order to work on much larger problems at much faster rates than dense algorithms. Nonetheless, optimizing these algorithms is not straightforward. Highly optimized algorithms for multiplying a sparse matrix by a dense vector, for instance, are the subject of a vast corpus of research and can be hundreds of times longer than naïve implementations. Optimized sparse linear algebra libraries are thus needed so that users can build applications without enormous effort. Hardware vendors release proprietary libraries that are highly optimized for their devices, but they limit interoperability and promote vendor lock-in. Open libraries often work across multiple devices and can quickly take advantage of new innovations, but they may not reach peak performance. The goal of this work is to provide a sparse linear algebra library that offers both of these advantages. We thus describe clSPARSE, a permissively licensed open-source sparse linear algebra library that offers state-of-the-art optimized algorithms implemented in OpenCL™. We test clSPARSE on GPUs from AMD and Nvidia and show performance benefits over both the proprietary cuSPARSE library and the open-source ViennaCL library.

Malecha Z.,Wroclaw University of Technology | Miroslaw L.,Vratis Ltd. | Miroslaw L.,Wroclaw University of Technology | Tomczak T.,Wroclaw University of Technology | And 5 more authors.
Archives of Mechanics | Year: 2011

THE SIMULATION OF BLOOD FLOW in the cardiac system has the potential to become an attractive diagnostic tool for many cardiovascular diseases, such as in the case of aneurysm. This potential could be reached if the simulations were to be completed in hours rather than days and without resorting to the use of expensive supercomputers. Therefore we have investigated a possibility of accelerating medical computational fluid dynamics (CFD) simulations using graphics processing units (GPUs). Our results for the 3D blood flow in the human abdominal aorta show that by transferring only a part of the computations (linear system solvers) to the GPU, it is possible to make the typical CFD simulations three to four times faster depending on the CFD model being used. Since these simulations were performed on widely available GPUs that had been designed as mass-market PC extension cards, our results suggest that porting larger parts of CFD to GPUs could really bring the technology into hospitals. Copyright © 2011 by IPPT PAN.

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