Estimation of Execution Parameters for k-Wave Simulations

Estimation of execution parameters takes centre stage in automatic offloading of complex biomedical workflows to cloud and high performance facilities. Since ordinary users have no or very limited knowledge of the performance characteristics of particular tasks in the workflow, the scheduling system has to have the capabilities to select appropriate amount of compute resources, e.g., compute nodes, GPUs, or processor cores and estimate the execution time and cost. The presented approach considers a fixed set of executables that can be used to create custom workflows, and collects performance data of successfully computed tasks. Since the workflows may differ in the structure and size of the input data, the execution parameters can only be obtained by searching the performance database and interpolating between similar tasks. This paper shows it is possible to predict the execution time and cost with a high confidence. If the task parameters are found in the performance database, the mean interpolation error stays below 2.29%. If only similar tasks are found, the mean interpolation error may grow up to 15%. Nevertheless, this is still an acceptable error since the cluster performance may vary on order of percent as well

Experimental validation of k-Wave: Nonlinear wave propagation in layered, absorbing fluid media

Models of ultrasound propagation in biologically relevant media have applications in planning and verification of ultrasound therapies and computational dosimetry. To be effective, the models must be able to accurately predict both the spatial distribution and amplitude of the acoustic pressure. This requires that the models are validated in absolute terms, which for arbitrarily heterogeneous media should be performed by comparison with measurements of the acoustic field. In this study, simulations performed using the open-source k-Wave acoustics toolbox, with a measurement-based source definition, were quantitatively validated against measurements of acoustic pressure in water and layered absorbing fluid media. In water, the measured and simulated spatial peak pressures agreed to within 3% under linear conditions and 7% under non-linear conditions. After propagation through a planar or wedge shaped glycerol-filled phantom, the difference in spatial peak pressure was 8.5% and 10.7%, respectively. These differences are within or close to the expected uncertainty of the acoustic pressure measurement. The -6 dB width and length of the focus agreed to within 4% in all cases, and the focal positions were within 0.7 mm for the planar phantom and 1.2 mm for the wedge shaped phantom. These results demonstrate that when the acoustic medium properties and geometry are well known, accurate quantitative predictions of the acoustic field can be made using k-Wave

Advanced photoacoustic image reconstruction using the k-Wave toolbox

Reconstructing images from measured time domain signals is an essential step in tomography-mode photoacoustic imaging. However, in practice, there are many complicating factors that make it difficult to obtain high-resolution images. These include incomplete or undersampled data, filtering effects, acoustic and optical attenuation, and uncertainties in the material parameters. Here, the processing and image reconstruction steps routinely used by the Photoacoustic Imaging Group at University College London are discussed. These include correction for acoustic and optical attenuation, spatial resampling, material parameter selection, image reconstruction, and log compression. The effect of each of these steps is demonstrated using a representative in vivo dataset. All of the algorithms discussed form part of the open-source k-Wave toolbox (available from http://www.k-wave.org)

Diagnostic accuracy of organ electrodermal diagnostics

Objective. To estimate the diagnostic accuracy as well as the scope of utilisation of a new bio-electronic method of organ diagnostics.Design. Double-blind comparative study of the diagnostic results obtained by means of organ electrodermal diagnostics (OED) and clinical diagnoses, as a criterion standard.Setting. Department of Surgery, Helen Joseph Hospital, Johannesburg.Patients. 70 pre-selected inpatients of mean age 36 (SD =7) years with suspected pathology of one (or more) of the following organs: oesophagus, stomach, duodenum, biliary tract, pancreas, colon, kidneys and urinary tract. In total, 276 of the above mentioned internal organs were selected for statistical consideration. Main outcome measures. The difference between the so-called basic electrical impedance of the skin and the impedance value established for a particular organ projection area (the skin zone corresponding to a particular internal organ).Results. In total 250 true OED results were obtained from the 276 subjects considered: detection rate 90.6% (95% Cl 87.1 - 94.1 %). Established OED sensitivity was 91.8% (95% Cl 88.6 - 95.0%) and OED specificity equalled 89.9% (95% Cl 86.4 - 93.4%). The predictive value for positive OED results was 83.3% (95% Cl 78.9 - 87.7%) and for negative OED results 95.2% (95% Cl 92.0 - 98.4%). The OED results were affected neither by the type nor the aetiology of disease, i.e. OED estimates the actual extent of the pathological process within particular organs but does not explain the cause of pathology directly. No sideeffects of the OED examinations were observed.Conclusions. So-called organ projection areas do exist on the skin surface. The electrical impedance of the projection areas corresponding to diseased organs is increased, relative to that of healthy organ-related skin zones. The difference in impedance is proportional to the intensity of the pathological process. OED, which utilises these electrical phenomena of the skin, may detect diseased organs and estimate the extent of pathological process activity within these organs

Nonlinear 3-D simulation of high-intensity focused ultrasound therapy in the Kidney

Kidney cancer is a severe disease which can be treated non-invasively using high-intensity focused ultrasound (HIFU) therapy. However, tissue in front of the transducer and the deep location of kidney can cause significant losses to the efficiency of the treatment. The effect of attenuation, refraction and reflection due to different tissue types on HIFU therapy of the kidney was studied using a nonlinear ultrasound simulation model. The geometry of the tissue was derived from a computed tomography (CT) dataset of a patient which had been segmented for water, bone, soft tissue, fat and kidney. The combined effect of inhomogeneous attenuation and soundspeed was found to result in an 11.0 dB drop in spatial peak-temporal average (SPTA) intensity in the kidney compared to pure water. The simulation without refraction effects showed a 6.3 dB decrease indicating that both attenuation and refraction contribute to the loss in focal intensity. The losses due to reflections at soft tissue interfaces were less than 0.1 dB. Focal point shifting due to refraction effects resulted in -1.3, 2.6 and 1.3 mm displacements in x-, y- and z-directions respectively. Furthermore, focal point splitting into several smaller subvolumes was observed. The total volume of the secondary focal points was approximately 46% of the largest primary focal point. This could potentially lead to undesired heating outside the target location and longer therapy times

Accurate simulation of transcranial ultrasound propagation for ultrasonic neuromodulation and stimulation

Non-invasive, focal neurostimulation with ultrasound is a potentially powerful neuroscientific tool that requires effective transcranial focusing of ultrasound to develop. Time-reversal (TR) focusing using numerical simulations of transcranial ultrasound propagation can correct for the effect of the skull, but relies on accurate simulations. Here, focusing requirements for ultrasonic neurostimulation are established through a review of previously employed ultrasonic parameters, and consideration of deep brain targets. The specific limitations of finite-difference time domain (FDTD) and k-space corrected pseudospectral time domain (PSTD) schemes are tested numerically to establish the spatial points per wavelength and temporal points per period needed to achieve the desired accuracy while minimizing the computational burden. These criteria are confirmed through convergence testing of a fully simulated TR protocol using a virtual skull. The k-space PSTD scheme performed as well as, or better than, the widely used FDTD scheme across all individual error tests and in the convergence of large scale models, recommending it for use in simulated TR. Staircasing was shown to be the most serious source of error. Convergence testing indicated that higher sampling is required to achieve fine control of the pressure amplitude at the target than is needed for accurate spatial targeting

Control of broadband optically generated ultrasound pulses using binary amplitude holograms

In this work, the use of binary amplitude holography is investigated as a mechanism to focus broadband acoustic pulses generated by high peak-power pulsed lasers. Two algorithms are described for the calculation of the binary holograms; one using ray-tracing, and one using an optimization based on direct binary search. It is shown using numerical simulations that when a binary amplitude hologram is excited by a train of laser pulses at its design frequency, the acoustic field can be focused at a pre-determined distribution of points, including single and multiple focal points, and line and square foci. The numerical results are validated by acoustic field measurements from binary amplitude holograms, excited by a high peak-power laser

Measurements of UV radiation on rotating vertical plane at the ALOMAR Observatory (69° N, 16° E), Norway, June 2007

International audienceErythemaly weighted UV and total UVA irradiance measured at the ALOMAR (Arctic Lidar Observatory for Middle Atmosphere Research; 69° N, 16° E) in June 2007 by two Kipp & Zonen UV broadband meters type, UV-S-AE-T, are examined. One unit is movable and mounted to rotating vertical plane, and the other is permanently fixed horizontally. The UV broadband meters measure simultaneously to allow the comparison of UV irradiances on vertical and horizontal plane. The entire range of relative exposure variations during clear-sky conditions over ALOMAR is examined using STAR and Radonic1 model (developed at the Meteorological Institute, Munich) for various action spectra (erythema, UVA, and vitamin D3). It seems that multiplication of the daily mean dose from a standard broadband meter placed horizontally by 0.5 gives reasonable estimation of the daily mean exposure on a vertical plane randomly oriented towards Sun. The extreme value and daily variability of relative exposure are the highest for UVA, next for UVB, then for vitamin D3 weighed UV irradiance. The minima of relative exposure (~0.20?0.30) are almost the same for all weighting functions. Specific cloud configuration could lead to significant enhancement of UV relative exposure of rotating plane being the most pronounced when biometer is in shadow. A statistical model is proposed, that it is able to simulate vitamin D3 weighted UV irradiances on vertical surface using explanatory variables: erythemal and total UVA irradiance from standard (horizontal) observations by Kipp & Zonen dual band biometer, the orientation of vertical plane, solar zenith angle, and column amount of total ozone. Statistical model will allow to reconstruct (or monitor) vitamin D3 weighted UV irradiances using available past (or actual) data