The Parallel Algorithm for the 2-D Discrete Wavelet Transform

The discrete wavelet transform can be found at the heart of many image-processing algorithms. Until now, the transform on general-purpose processors (CPUs) was mostly computed using a separable lifting scheme. As the lifting scheme consists of a small number of operations, it is preferred for processing using single-core CPUs. However, considering a parallel processing using multi-core processors, this scheme is inappropriate due to a large number of steps. On such architectures, the number of steps corresponds to the number of points that represent the exchange of data. Consequently, these points often form a performance bottleneck. Our approach appropriately rearranges calculations inside the transform, and thereby reduces the number of steps. In other words, we propose a new scheme that is friendly to parallel environments. When evaluating on multi-core CPUs, we consistently overcome the original lifting scheme. The evaluation was performed on 61-core Intel Xeon Phi and 8-core Intel Xeon processors.Comment: accepted for publication at ICGIP 201

On-the-Fly Calculation of Time-Averaged Acoustic Intensity in Time-Domain Ultrasound Simulations Using a k-Space Pseudospectral Method

OBJECTIVE: This paper presents a method to calculate the average acoustic intensity during ultrasound simulation using a new approach that exploits compression of intermediate results. METHODS: One of the applications of high-intensity focused ultrasound (HIFU) simulations is the calculation of the thermal dose, which indicates the amount of tissue destroyed using a state-of-the-art k-space pseudospectral method. The thermal simulation is preceded by the calculation of the average intensity within the acoustic simulation. Due to the time staggering between the particle velocity and the acoustic pressure used in such simulations, the average intensity calculation is typically executed offline after the acoustic simulation consuming both disk space and time (the data can spread over terabytes). Our new approach calculates the average intensity during the acoustic simulation using the output coefficients of a new compression method which enables resolving the time staggering on-the-fly with huge disk space savings. To reduce RAM requirements, the article also presents a new 40-bit method for encoding compression complex coefficients. RESULTS: Experimental numerical simulations with the proposed method have shown that disk space requirements are up to 99 % lower. The simulation speed was not significantly affected by the approach and the compression error did not affect the prediction accuracy of the thermal dose. CONCLUSION: From the standpoint of supercomputers, the new approach is significantly more economical. SIGNIFICANCE: Saving computing resources increases the chances of real use of acoustic simulations in practice. The method can be applied to signals of a similar character, e.g., for electromagnetic radio waves

Automated high‐speed CE system for multiple samples

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/96756/1/elps4558.pd

Viability analysis and apoptosis induction of breast cancer cells in a microfluidic device: effect of cytostatic drugs

Breast cancer is the leading cause of cancer deaths among non-smoking women worldwide. At the moment the treatment regime is such that patients receive different chemotherapeutic and/or hormonal treatments dependent on the hormone receptor status, the menopausal status and age. However, in vitro sensitivity testing of tumor biopsies could rationalize and improve the choice of chemo- and hormone therapy. Lab-on-a-Chip devices, using microfluidic techniques, make detailed cellular analysis possible using fewer cells, enabling working with a patients’ own cells and performing chemo- and hormone sensitivity testing in an ex vivo setting. This article describes the development of two microfluidic devices made in poly(dimethylsiloxane) (PDMS) to validate the cell culture properties and analyze the chemosensitivity of MCF-7 cells (estrogen receptor positive human breast cancer cells) in response to the drug staurosporine (SSP). In both cases, cell viability was assessed using the life-stain Calcein-AM (CAAM) and the death dye propidium iodide (PI). MCF-7 cells could be statically cultured for up to 7 days in the microfluidic chip. A 30 min flow with SSP and a subsequent 24 h static incubation in the incubator induced apoptosis in MCF-7 cells, as shown by a disappearance of the aggregate-like morphology, a decrease in CAAM staining and an increase in PI staining. This work provides valuable leads to develop a microfluidic chip to test the chemosensitivity of tumor cells in response to therapeutics and in this way improve cancer treatment towards personalized medicine

Comparison of two dimensional computer codes on the case study of the flow computation of the river Bolska near Gomilsko

V diplomski nalogi so z dvodimenzijskimi programi PCFLOW2D, MIKE 21 ter MIKE Flood izvedeni izračuni z različnimi pretoki za reko Bolsko pri Gomilskem. Na začetku sta opisana vodotoka Bolska in Trnavca ter računsko območje, ki je bilo modelirano. Izveden je bil tudi terenski ogled območja, da se je nato lažje določilo različne koeficiente. V nadaljevanju so opisane teoretične osnove računanja pri uporabljenih programih ter priprava računskega modela za posamezne programe. Na podlagi zahtevnosti vnosa računskega modela ter dobljenih rezultatov so na koncu podane prednosti in slabosti posameznih programov ter analizirane razlike v izračunanih poljih hitrosti in globinah.In this diploma thesis, I carried out calculations of various flows for the Bolska river below the town of Gomilsko by two-dimensional programmes PCFLOW 2D, MIKE 21, and MIKE Flood. In the beginning, the Bolska and Trnavca watershed and modelled calculation domain are described. I also performed site surveys of the area in order to define various coefficients more effectively. Moreover, the background of the calculation of specific programmes and the preparation of the calculation model for individual programme is briefly described. Based on the complexity of the input of the calculation model and the obtained results, I finally set out the advantages and weaknesses of each programme and analysed the differences of calculated velocity fields and water depths