Publications

2020

Journal Articles

M. Bakaric, P. Miloro, B. Zeqiri, B. T. Cox, B. E. Treeby

The effect of curing temperature and time on the acoustic and optical properties of PVCP Journal Article

IEEE Trans. Ultrason. Ferroelectr. Freq. Control, 67 (3), pp. 505-512, 2020.

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D. R. Ramasawmy, B. T. Cox, B. E. Treeby

ElasticMatrix: A MATLAB toolbox for anisotropic elastic wave propagation in layered media Journal Article

SoftwareX, 11 , pp. 100397, 2020.

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E. Martin, J. Jaros, B. E. Treeby

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

IEEE Trans. Ultrason. Ferroelectr. Freq. Control, 67 (1), pp. 81-91, 2020.

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Conferences

M. Bakaric, B. Zeqiri, B. T. Cox, B. E. Treeby

Test materials for characterising heating from HIFU devices using photoacoustic thermometry Conference

Proc. SPIE, Photons Plus Ultrasound: Imaging and Sensing 2020, 11240 , 2020.

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2019

Journal Articles

M. D. Brown

Phase and amplitude modulation with acoustic holograms Journal Article

Appl. Phys. Lett., 115 , pp. 053701, 2019.

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E. S. Wise, B. T. Cox, J. Jaros, B. E. Treeby

Representing arbitrary acoustic source and sensor distributions in Fourier collocation methods Journal Article

J. Acoust. Soc. Am., 146 (1), pp. 278-288, 2019.

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M. D. Brown, E. Z. Zhang, B. E. Treeby, P. C. Beard, B. T. Cox

Reverberant cavity photoacoustic imaging Journal Article

Optica, 6 (6), pp. 821-822, 2019.

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B. E. Treeby, J. Jaros, E. Martin, B. T. Cox

From biology to bytes: Predicting the path of ultrasound waves through the human body Journal Article

Acoustics Today, 15 (2), pp. 36-44, 2019.

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D. R. Ramasawmy, E. Martin, J. A. Guggenheim, E. Z. Zhang, P. C. Beard, B. E. Treeby, B. T. Cox

Analysis of the Directivity of Glass-Etalon Fabry-Perot Ultrasound Sensors Journal Article

IEEE Trans. Ultrason. Ferroelectr. Freq. Control, 66 (9), pp. 1504-1513, 2019.

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E. Martin, B. E. Treeby

Investigation of the repeatability and reproducibility of hydrophone measurements of medical ultrasound fields Journal Article

J. Acoust. Soc. Am., 145 (3), pp. 1270-1282, 2019.

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Conferences

L. Albelda Gimeno, E. Martin, O. Wright, B. E. Treeby

Experimental assessment of skull aberration and transmission loss at 270 kHz for focused ultrasound stimulation of the primary visual cortex Conference

IEEE International Ultrasonics Symposium, 2019.

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M. Bakaric, A. Ivory, B. Zeqiri, B. T. Cox, B. E. Treeby

Measurement of the temperature-dependent speed of sound and change in Gruneisen parameter of tissue-mimicking materials Conference

IEEE International Ultrasonics Symposium, 2019.

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D. R. Ramasawmy, B. T. Cox, B. E. Treeby

The influence of strain-optic coefficients on the transduction mechanism of planar glass etalon Fabry-Perot ultrasound sensors Conference

IEEE International Ultrasonics Symposium, 2019.

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F. Vaverka, B. E. Treeby, J. Jaros

Evaluation of the suitability of Intel Xeon Phi clusters for the simulation of ultrasound wave propagation using pseudospectral methods Conference

International Conference on Computational Science (ICCS 2019), LNCS, , 11538 , 2019.

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2018

Journal Articles

V. Suomi, J. Jaros, B. E. Treeby, R. Cleveland

Full modeling of high-intensity focused ultrasound and thermal heating in the kidney using realistic patient models Journal Article

IEEE Trans. Biomed. Eng., 65 (11), pp. 2660-2670, 2018.

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V. Suomi, B. E. Treeby, J. Jaros, P. Makela, M. Anttinen, J. Saunavaara, T. Sainio, A. Kiviniemi, R. Blanco

Transurethral ultrasound therapy of the prostate in the presence of calcifications: A simulation study Journal Article

Med. Phys., 45 (11), pp. 4793-4805, 2018.

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E. S. Wise, B. T. Cox, B. E. Treeby

Bandwidth-based mesh adaptation in multiple dimensions Journal Article

J. Comp. Phys., 371 , pp. 651-662, 2018.

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B. E. Treeby, F. Lucka, E. Martin, B. T. Cox

Equivalent-source acoustic holography for projecting measured ultrasound fields through complex media Journal Article

IEEE Trans. Ultrason. Ferroelectr. Freq. Control, 65 (10), pp. 1857-1864, 2018.

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B. E. Treeby, E. S. Wise, B. T. Cox

Nonstandard Fourier Pseudospectral Time Domain (PSTD) Schemes for Partial Differential Equations Journal Article

Commun. Comput. Phys., 24 (3), pp. 623-634, 2018.

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S. Rajagopal, T. Sainsbury, B. E. Treeby, B. T. Cox

Laser generated ultrasound sources using carbon-polymer nanocomposites for high frequency metrology Journal Article

J. Acoust. Soc. Am., 144 (2), pp. 584-597, 2018.

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J. L. Robertson, J. Urban, J. Stitzel, B. E. Treeby

The effects of image homogenisation on simulated transcranial ultrasound propagation Journal Article

Phys. Med. Biol., 63 , pp. 145014, 2018.

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M. Bakaric, E. Martin, P. S. Georgiou, B. T. Cox, H. Payne, B. E. Treeby

Experimental study of beam distortion due to fiducial markers during salvage HIFU in the prostate Journal Article

Journal of Therapeutic Ultrasound, 6 (1), pp. 1-12, 2018.

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B. E. Treeby, J. Budisky, E. S. Wise, J. Jaros, B. T. Cox

Rapid calculation of acoustic fields from arbitrary continuous-wave sources Journal Article

J. Acoust. Soc. Am., 143 (1), pp. 529-537, 2018.

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Conferences

B. T. Cox, B. E. Treeby

Accurate time-varying sources in k-space pseudospectral time domain acoustic simulations Conference

IEEE International Ultrasonics Symposium, 2018.

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B. E. Treeby, F. Vaverka, J. Jaros

Performance and accuracy analysis of nonlinear k-Wave simulations using local domain decomposition with an 8-GPU server Conference

Proc. Mtgs. Acoust., 34 , 2018.

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V. Suomi, B. E. Treeby, J. Jaros, J. Saunavaara, A. Kiviniemi, R. Blanco

The effect of tissue physiological variability on transurethral ultrasound therapy of the prostate Conference

40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 2018.

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K. Kadlubiak, J. Jaros, B. E. Treeby

GPU-Accelerated Simulation of Elastic Wave Propagation Conference

2018 International Conference on High Performance Computing & Simulation (HPCS), IEEE, 2018.

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M. Cudova, B. E. Treeby, J. Jaros

Design of HIFU treatment plans using an evolutionary strategy Conference

Proceedings of the Genetic and Evolutionary Computation Conference (GECCO) Companion, 2018.

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2017

Journal Articles

M. D. Brown, B. T. Cox, B. E. Treeby

Design of multi-frequency acoustic kinoforms Journal Article

Appl. Phys. Lett., 111 (24), pp. 244101, 2017.

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E. Martin, E. Z. Zhang, J. A. Guggenheim, P. C. Beard, B. E. Treeby

Rapid spatial mapping of focused ultrasound fields using a planar Fabry-Perot sensor Journal Article

IEEE Trans. Ultrason. Ferroelectr. Freq. Control, 64 (11), pp. 1711-1722, 2017.

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E. S. Wise, B. T. Cox, B. E. Treeby

Mesh density functions based on local bandwidth applied to moving mesh methods Journal Article

Commun. Comput. Phys., 22 (5), pp. 1286-1308, 2017.

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J. L. Robertson, B. T. Cox, J. Jaros, B. E. Treeby

Accurate simulation of transcranial ultrasound propagation for ultrasonic neuromodulation and stimulation Journal Article

J. Acoust. Soc. Am., 141 (3), pp. 1726-1738, 2017.

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M. Perez Liva, J. L. Herraiz, J. M. Udias, E. Miller, B. T. Cox, B. E. Treeby

Time domain reconstruction of sound speed and attenuation in ultrasound computed tomography using full wave inversion Journal Article

J. Acoust. Soc. Am., 141 (3), pp. 1595-1604, 2017.

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J. L. Robertson, E. Martin, B. T. Cox, B. E. Treeby

Sensitivity of simulated transcranial ultrasound fields to acoustic medium property maps Journal Article

Phys. Med. Biol., 62 (7), pp. 2559-2580, 2017.

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M. D. Brown, D. I. Nikitichev, B. E. Treeby, B. T. Cox

Generating arbitrary ultrasound fields with tailored optoacoustic surface profiles Journal Article

Appl. Phys. Lett., 110 (9), pp. 094102, 2017.

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P. S. Georgiou, J. Jaros, H. Payne, C. Allen, T. T. Shah, H. U. Ahmed, E. Gibson, D. Barratt, B. E. Treeby

Beam distortion due to gold fiducial markers during salvage high-intensity focused ultrasound in the prostate Journal Article

Med. Phys., 44 (2), pp. 679–693, 2017.

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Conferences

M. D. Brown, B. T. Cox, B. E. Treeby

Investigating the effect of thickness and frequency spacing on multi-frequency acoustic kinoforms Conference

IEEE International Ultrasonics Symposium, 2017.

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S. Rajagopal, T. Sainsbury, B. E. Treeby, B. T. Cox

Laser generated ultrasound sources using polymer nanocomposites for high frequency metrology Conference

IEEE International Ultrasonics Symposium, 2017.

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E. S. Wise, J. L. Robertson, B. T. Cox, B. E. Treeby

Staircase-free acoustic sources for grid-based models of wave propagation Conference

IEEE International Ultrasonics Symposium, 2017.

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D. R. Ramasawmy, E. Martin, J. A. Guggenheim, B. T. Cox, B. E. Treeby

Directivity of a planar hard-dielectric Fabry-Perot optical ultrasound sensor Conference

IEEE International Ultrasonics Symposium, 2017.

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2016

Journal Articles

J. Jaros, F. Vaverka, B. E. Treeby

Spectral domain decomposition using local Fourier basis: Application to ultrasound simulation on a cluster of GPUs Journal Article

Supercomputing Frontiers and Innovations, 3 (3), pp. 39–54, 2016.

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S. R. Arridge, M. M. Betcke, B. T. Cox, F. Lucka, B. E. Treeby

On the adjoint operator in photoacoustic tomography Journal Article

Inv. Problems, 32 (11), pp. 115012, 2016.

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E. Martin, Y. T. Ling, B. E. Treeby

Simulating focused ultrasound transducers using discrete sources on regular cartesian grids Journal Article

IEEE Trans. Ultrason. Ferroelectr. Freq. Control, 63 (10), pp. 1535–1542, 2016.

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J. Jaros, A. P. Rendell, B. E. Treeby

Full-wave nonlinear ultrasound simulation on distributed clusters with applications in high-intensity focused ultrasound Journal Article

Int. J. High Perform. Comput., 30 (2), pp. 137–155, 2016.

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M. D. Brown, J. Jaros, B. T. Cox, B. E. Treeby

Control of broadband optically generated ultrasound pulses using binary amplitude holograms Journal Article

J. Acoust. Soc. Am., 139 (4), pp. 1637–1467, 2016.

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Conferences

M. D. Brown, E. Martin, B. T. Cox, B. E. Treeby

Single pulse illumination of multi-layer photoacoustic holograms for patterned ultrasound field generation Conference

IEEE International Ultrasonics Symposium, 2016.

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V. Suomi, J. Jaros, B. E. Treeby, R. Cleveland

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

IEEE 38th Annual International Conference of the Engineering in Medicine and Biology Society (EMBC), 2016.

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M. Perez Liva, J. L. Herraiz, J. M Udias, B. T. Cox, B. E. Treeby

Full-wave attenuation reconstruction in the time domain for ultrasound computed tomography Conference

IEEE 13th International Symposium on Biomedical Imaging (ISBI), 2016.

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B. E. Treeby, J. Jaros, B. T. Cox

Advanced photoacoustic image reconstruction using the k-Wave toolbox Conference

Proc. SPIE, Photons Plus Ultrasound: Imaging and Sensing, 9708 , 2016.

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2015

Journal Articles

A. P. Jathoul, J. Laufer, O. Ogunlade, B. E. Treeby, B. T. Cox, E. Z. Zhang, P. Johnson, A. R. Pizzey, B. Philip, T. Marafioti, M. F. Lythgoe, R. B. Pedley, M. A. Pule, P. C. Beard

Deep in vivo photoacoustic imaging of mammalian tissues using a tyrosinase-based genetic reporter Journal Article

Nature Photonics, 9 , pp. 239–-246, 2015.

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Conferences

Y. T. Ling, E. Martin, B. E. Treeby

Discrete source model for simulating bowl-shaped focused ultrasound transducers on regular grids: Design and experimental validation Conference

IEEE International Ultrasonics Symposium, 2015.

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E. Martin, E. Z. Zhang, P. C. Beard, B. E. Treeby

Rapid spatial mapping of the acoustic pressure in high intensity focused ultrasound fields at clinical intensities using a novel planar Fabry-Perot interferometer Conference

IEEE International Ultrasonics Symposium, 2015.

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B. E. Treeby, T. Saratoon

The contribution of shear wave absorption to ultrasound heating in bones: Coupled elastic and thermal modeling Conference

IEEE International Ultrasonics Symposium, 2015.

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E. S. Wise, B. T. Cox, B. E. Treeby

A monitor function for spectral moving mesh methods applied to nonlinear acoustics Conference

International Symposium on Nonlinear Acoustics (AIP Conference Proceedings), 1685 , 2015.

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E. Martin, B. E. Treeby

Experimental validation of computational models for large-scale nonlinear ultrasound simulations in heterogeneous, absorbing fluid media Conference

International Symposium on Nonlinear Acoustics (AIP Conference Proceedings), 1685 , 2015.

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J. Jaros, V. Nikl, B. E. Treeby

Large-scale ultrasound simulations using the hybrid OpenMP/MPI decomposition Conference

Proceedings of the 3rd International Conference on Exascale Applications and Software, 2015, ISBN: 978-0-9926615-1-9.

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2014

Journal Articles

B. E. Treeby, B. T. Cox

Modeling power law absorption and dispersion in viscoelastic solids using a split-field and the fractional Laplacian Journal Article

J. Acoust. Soc. Am., 136 (4), pp. 1499-1510, 2014.

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Conferences

M. D. Brown, T. J. Allen, B. T. Cox, B. E. Treeby

Control of optically generated ultrasound fields using binary amplitude holograms Conference

IEEE International Ultrasonics Symposium, 2014.

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J. L. Robertson, B. T. Cox, B. E. Treeby

Quantifying numerical errors in the simulation of transcranial ultrasound using pseudospectral methods Conference

IEEE International Ultrasonics Symposium, 2014.

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L. Demi, B. E. Treeby, M. D. Verweij

Comparison between two different full-wave methods for the computation of nonlinear ultrasound fields in inhomogeneous and attenuating tissue Conference

IEEE International Ultrasonics Symposium, 2014.

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B. E. Treeby, J. Jaros, D. Rohrbach, B. T. Cox

Modelling elastic wave propagation using the k-Wave MATLAB toolbox Conference

IEEE International Ultrasonics Symposium, 2014.

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Book Chapters

M. D. Verweij, B. E. Treeby, K. W. A. van Dongen, L. Demi

Simulation of Ultrasound Fields Book Chapter

Panetta, D; Demi, M (Ed.): Comprehensive Biomedical Physics, 2 , Chapter 19, pp. 465–500, Elsevier, Amsterdam, 2014.

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2013

Journal Articles

B. E. Treeby

Modeling nonlinear wave propagation on nonuniform grids using a mapped k-space pseudospectral method Journal Article

IEEE Trans. Ultrason. Ferroelectr. Freq. Control, 60 (10), pp. 2208–2213, 2013.

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B. E. Treeby

Acoustic attenuation compensation in photoacoustic tomography using time-variant filtering Journal Article

J. Biomed. Opt., 18 (3), pp. 036008, 2013.

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Conferences

E. S. Wise, B. E. Treeby

Full-wave nonlinear ultrasound simulation in an axisymmetric coordinate system using the discrete sine and cosine transforms Conference

IEEE International Ultrasonics Symposium, 2013.

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B. E. Treeby, B. T. Cox

A computationally efficient elastic wave model for media with power-law absorption Conference

IEEE International Ultrasonics Symposium, 2013.

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T. Oruganti, J. Laufer, B. E. Treeby

Vessel filtering of photoacoustic images Conference

Proc. SPIE, Photons Plus Ultrasound: Imaging and Sensing, 8581 , 2013.

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2012

Journal Articles

K. Firouzi, B. T. Cox, B. E. Treeby, N. Saffari

A first-order k-space model for elastic wave propagation in heterogeneous media Journal Article

J. Acoust. Soc. Am., 132 (3), pp. 1271–1283, 2012.

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B. E. Treeby, J. Jaros, A. P. Rendell, B. T. Cox

Modeling nonlinear ultrasound propagation in heterogeneous media with power law absorption using a k-space pseudospectral method Journal Article

J. Acoust. Soc. Am., 131 (6), pp. 4324–4336, 2012.

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Conferences

N. Nandapalan, J. Jaros, A. P. Rendell, B. E. Treeby

Implementation of 3D FFTs across multiple GPUs in shared memory environments Conference

13th International Conference on Parallel and Distributed Computing, Applications and Technologies (PDCAT), 2012.

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K. Wang, E. Teoh, J. Jaros, B. E. Treeby

Modelling nonlinear ultrasound propagation in absorbing media using the k-Wave toolbox: Experimental validation Conference

IEEE International Ultrasonics Symposium, 2012.

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A. Haigh, B. E. Treeby, E. McCreath

Ultrasound simulation on the cell broadband engine using the Westervelt equation Conference

12th International Conference on Algorithms and Architectures for Parallel Processing, Part 1, LNCS, 7439 , 2012.

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J. Jaros, B. E. Treeby, A. P. Rendell

Use of multiple GPUs on shared memory multiprocessors for ultrasound propagation simulations Conference

10th Australasian Symposium on Parallel and Distributed Computing, 127 , 2012, ISBN: 978-1-921770-08-1.

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2011

Journal Articles

B. E. Treeby, T. K. Varslot, E. Z. Zhang, J. Laufer, P. C. Beard

Automatic sound speed selection in photoacoustic image reconstruction using an autofocus approach Journal Article

J. Biomed. Opt., 16 (9), pp. 090501, 2011.

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B. E. Treeby, B. T. Cox

A k-space Green's function solution for acoustic initial value problems in homogeneous media with power law absorption Journal Article

J. Acoust. Soc. Am., 129 (6), pp. 3652–3660, 2011.

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B. E. Treeby, E. Z. Zhang, A. S. Thomas, B. T. Cox

Measurement of the ultrasound attenuation and dispersion in whole human blood and its components from 0-70 MHz Journal Article

Ultrasound Med. Biol., 37 (2), pp. 289–300, 2011.

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Conferences

B. E. Treeby, M. Tumen, B. T. Cox

Time domain simulation of harmonic ultrasound images and beam patterns in 3D using the k-space pseudospectral method Conference

14th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Part I, LNCS, 6891 , 2011.

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B. E. Treeby, J. Laufer, E. Z. Zhang, F. C. Norris, M. F. Lythgoe, P. C. Beard, B. T. Cox

Acoustic attenuation compensation in photoacoustic tomography: Application to high resolution 3D imaging of vascular networks in mice Conference

Proc. SPIE, Photons Plus Ultrasound: Imaging and Sensing, 7899 , 2011.

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2010

Journal Articles

B. E. Treeby, B. T. Cox

k-Wave: MATLAB toolbox for the simulation and reconstruction of photoacoustic wave-fields Journal Article

J. Biomed. Opt., 15 (2), pp. 021314, 2010.

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B. T. Cox, B. E. Treeby

Artifact trapping during time reversal photoacoustic imaging for acoustically heterogeneous media Journal Article

IEEE Trans. Med. Imaging, 29 (2), pp. 387–396, 2010.

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B. E. Treeby, B. T. Cox

Modeling power law absorption and dispersion for acoustic propagation using the fractional Laplacian Journal Article

J. Acoust. Soc. Am., 127 (5), pp. 2741–2748, 2010.

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B. E. Treeby, E. Z. Zhang, B. T. Cox

Photoacoustic tomography in absorbing acoustic media using time reversal Journal Article

Inverse Probl., 26 (11), pp. 115003, 2010.

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Conferences

B. T. Cox, B. E. Treeby

Effect of sensor directionality on photoacoustic imaging: a study using the k-Wave toolbox Conference

Proc. SPIE, Photons Plus Ultrasound: Imaging and Sensing, 7564 , 2010.

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2009

Journal Articles

B. E. Treeby, B. T. Cox, E. Z. Zhang, S. K. Patch, P. C. Beard

Measurement of broadband temperature-dependent ultrasonic attenuation and dispersion using photoacoustics Journal Article

IEEE Trans. Ultrason. Ferroelectr. Freq. Control, 56 (8), pp. 1666–1676, 2009.

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Conferences

B. E. Treeby, B. T. Cox

Fast, tissue-realistic models of photoacoustic wave propagation for homogeneous attenuating media Conference

Proc. SPIE, Photons Plus Ultrasound: Imaging and Sensing, 7177 , 2009.

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2007

Journal Articles

B. T. Cox, S. Kara, S. R. Arridge, P. C. Beard

k-space propagation models for acoustically heterogeneous media: Application to biomedical photoacoustics Journal Article

J. Acoust. Soc. Am., 121 (6), pp. 3453–3464, 2007.

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2005

Journal Articles

B. T. Cox, P. C. Beard

Fast calculation of pulsed photoacoustic fields in fluids using k-space methods Journal Article

J. Acoust. Soc. Am., 117 (6), pp. 3616–3627, 2005.

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2004

Conferences

B. T. Cox, J. Laufer, K. P. Kostli, P. C. Beard

Experimental validation of photoacoustic k-space propagation models Conference

Proc. SPIE, Photons Plus Ultrasound: Imaging and Sensing, 5320 , 2004.

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