News - Publications

PAMMOTH publications

June 2020
Spatially compounded plane wave imaging using a laser-induced ultrasound source
David Thompson, Damien Gasteau, Srirang Manohar
Photoacoustics, Volume 18, 100154, http://dx.doi.org/10.1016/j.pacs.2019.100154


March 2020
Quantitative comparison of frequency-domain and delay-and-sum optoacoustic image reconstruction including the effect of coherence factor weighting
Florentin Spadin, Michael Jaeger, Robert Nuster, Pavel Subochev, Martin Frenz
Photoacoustics, Volume 17, 100149, https://doi.org/10.1016/j.pacs.2019.100149


January 2020
A Partially-Learned Algorithm for Joint Photo-acoustic Reconstruction and Segmentation
Marta Cudova, Bradley E Treeby, Jiří Jaroš
IEEE Transactions on Medical Imaging, vol. 39, no. 1, pp. 129-139, DOI:10.1109/TMI.2019.2922026


December 2019
Estimating blood oxygenation from photoacoustic images: can a simple linear spectroscopic inversion ever work?
Roman Hochuli, Lu An, Paul C. Beard, Benjamin T. Cox
J. of Biomedical Optics 24(12), 24(12) 121914, https://doi.org/10.1117/1.JBO.24.12.121914


December 2019
Current and future trends in photoacoustic breast imaging
Srirang Manohar, Maura Dantuma
Photoacoustics, Volume 16, 100134, http://dx.doi.org/10.1016/j.pacs.2019.04.004


November 2019
Adaptive Execution Planning in Biomedical Workflow Management Systems
Marta Jaros, Bradley E. Treeby, Jiri Jaros
SC19: The International Conference for High Performance Computing, Networking, Storage, and Analysis


November 2019
Advancements in Ultrasound Simulations Enabled by High-Bandwidth GPU Interconnects
Filip Vaverka, Bradley E. Treeby, Jiri Jaros
SC19: The International Conference for High Performance Computing, Networking, Storage, and Analysis


October 2019
Twente Photoacoustic Mammoscope 2: system overview and three-dimensional vascular network images in healthy breasts
Sjoukje M. Schoustra, Daniele Piras, Roeland Huijink, Tim J. P. M. op ‘t Root, Laurens Alink, Wouter Muller Kobold, Wiendelt Steenbergen, Srirang Manohar
Journal of Biomedical Optics, 24(12), 121909 (2019), https://doi.org/10.1117/1.JBO.24.12.121909


October 2019
A semi-anthropomorphic breast phantom with tunable blood oxygenation levels for use in quantitative photoacoustics
Maura Dantuma, Javier Ortega Julia, Srirang Manohar
TENCON 2019 - 2019 IEEE Region 10 Conference (TENCON), pages 114-117


September 2019
Single-pixel camera photoacoustic tomography
Nam Huynh, Felix Lucka, Edward Z. Zhang, Marta M. Betcke, Simon R. Arridge, Paul C. Beard, Benjamin T. Cox
J. of Biomedical Optics 24(12), 121907, https://doi.org/10.1117/1.JBO.24.12.121907


July 2019
Representing arbitrary acoustic source and sensor distributions in Fourier collocation methods
Elliott S. Wise, B. T. Cox, Jiri Jaros, Bradley E. Treeby
The Journal of the Acoustical Society of America 146, 278 (2019); https://doi.org/10.1121/1.5116132


July 2019
Laser-induced ultrasound transmitters for 3D photoacoustic and ultrasound tomography
Damien Gasteau, David Thompson, Srirang Manohar
Proc. SPIE 11077, Opto-Acoustic Methods and Applications in Biophotonics IV, 1107716 (19 July 2019), page 41


June 2019
Evaluation of the Suitability of Intel Xeon Phi Clusters for the Simulation of Ultrasound Wave Propagation Using Pseudospectral Methods
Filip Vaverka, Bradley E. Treeby, Jiri Jaros
Computational Science – ICCS 2019 - 19th International Conference, Faro, Portugal, June 12–14, 2019, Proceedings, Part III, pp. 577-590, https://doi.org/10.1007/978-3-030-22744-9_45


March 2019
Robustness of a partially learned photoacoustic reconstruction algorithm
Yoeri Boink, Christoph Brune, Srirang Manohar
Proc. SPIE 10878, Photons Plus Ultrasound: Imaging and Sensing 2019, 108781D (6 March 2019), page 47


March 2019
Breast tumor appearances in photoacoustic tomography from fine 3D optical-acoustic simulations (Conference Presentation)
Maura Dantuma, Felix Lucka, Jiri Jaros, Bradley E. Teeby, Ben T. Cox, Srirang Manohar
Proc. SPIE 10878, Photons Plus Ultrasound: Imaging and Sensing 2019, 108781I (4 March 2019), page 52


March 2019
International Photoacoustic Standardisation Consortium (IPASC): overview (Conference Presentation)
Sarah Bohndiek, Joanna Brunker, Janek Gröhl, Lina Hacker, James Joseph, William C. Vogt, Paolo Armanetti, Hisham Assi, Jeffrey C. Bamber, Paul C. Beard, Thomas Berer, Richard Bouchard, Kimberly A. Briggman, Lucia Cavigli, Bryan Clingman, Ben T. Cox, Adrien E. Desjardins, Andrew Heinmiller, Jeesong Hwang, Eno Hysi, Aoife Ivory, Jithin Jose, Thomas Kirchner, Jan Klohs, Lena Maier-Hein, Efthymios Maneas, Julia Mannheim, Srirang Manohar, Lacey McNally, Luca Menichetti, Steven Miller, Stefan Morscher, Ruiqing Ni, Yoko Okamura, Malini C. Olivo, Marty Pagel, Geoff Parker, Anna Pelagotti, Antonio Pifferi, Srinath Rajagopal, Fulvio Ratto, Daniel Razansky, Lisa M. Richards, Avihai Ron, Mithun Kuniyil Ajith Singh, Maximillian Waldner, Kun Wang, Lihong V. Wang, Wenfeng Xia, Bajram Zeqiri
Proc. SPIE 10878, Photons Plus Ultrasound: Imaging and Sensing 2019, 108781N (4 March 2019), page 57


March 2019
Plane wave and synthetic transmit aperture echography using laser-induced ultrasound (Conference Presentation)
David Thompson, Libertario Demi, Erik Kruit, Damien Gasteau, Marieke Olsman, Srirang Manohar
Proc. SPIE 10878, Photons Plus Ultrasound: Imaging and Sensing 2019, 108781A (4 March 2019), page 44


February 2019
A 3D semi-anthropomorphic photoacoustic breast phantom
Maura Dantuma, Rianne van Dommelen, Srirang Manohar
Proc. SPIE 10878, Photons Plus Ultrasound: Imaging and Sensing 2019, 108781P (27 February 2019), page 59


February 2019
The Twente Photoacoustic Mammoscope 2: 3D vascular network visualization
Sjoukje M. Schoustra, Roeland Huijink, Laurens Alink, Tim J. P. M. op 't Root, Daan Sprünken, Daniele Piras, Wouter F. Muller Kobold, Caroline A. H. Klazen, Margreet C. van der Schaaf, Frank M. van den Engh, Wiendelt Steenbergen, Srirang Manohar
Proc. SPIE 10878, Photons Plus Ultrasound: Imaging and Sensing 2019, 1087813 (27 February 2019), page 37


February 2019
Forward model for quantitative pulse-echo speed-of-sound imaging
Stähli, Patrick; Kuriakose, Maju; Frenz, Martin; Jaeger, Michael
Cornell University, Ithaca, New York, http://arxiv.org/abs/1902.10639


2019
Semi-anthropomorphic photoacoustic breast phantom
Maura Dantuma, Rianne van Dommelen, Srirang Manohar
Biomedical Optics Express Vol. 10, Issue 11, pp. 5921-5939 (2019), https://doi.org/10.1364/BOE.10.005921


October 2018
Effect of Backing on Carbon-Polymer Nanocomposite Sources for Laser Generation of Broadband Ultrasound Pulses
S. Rajagopal, B. E. Treeby and B. T. Cox
2018 IEEE International Ultrasonics Symposium (IUS), Kobe, 2018, pp. 1-4, https://doi.org/10.1109/ULTSYM.2018.8579784


October 2018
Accurate Time-Varying Sources in K-Space Pseudospectral Time Domain Acoustic Simulations
B. T. Cox and B. E. Treeby
2018 IEEE International Ultrasonics Symposium (IUS), Kobe, 2018, pp. 1-4, https://doi.org/10.1109/ULTSYM.2018.8580206


October 2018
Enhancing Compressed Sensing 4D Photoacoustic Tomography by Simultaneous Motion Estimation
Felix Lucka, Nam Huynh, Marta Betcke, Edward Zhang, Paul Beard, Ben Cox, Simon Arridge
SIAM Journal on Imaging Sciences, Volume 11, Issue 4, 2224–2253, https://doi.org/10.1137/18M1170066


September 2018
Real-time cardiovascular MR with spatio-temporal artifact suppression using deep learning–proof of concept in congenital heart disease
Andreas Hauptmann, Simon Arridge, Felix Lucka, Vivek Muthurangu, Jennifer A. Steeden
Magnetic Resonance in Medicine, Volume 81, Issue 2, pages 1143-1156, https://doi.org/10.1002/mrm.27480


August 2018
Equivalent-Source Acoustic Holography for Projecting Measured Ultrasound Fields Through Complex Media
B. Treeby, F. Lucka, E. Martin and B. T. Cox
IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, vol. 65, no. 10, pp. 1857-1864, https://doi.org/10.1109/TUFFC.2018.2861895


August 2018
Laser generated ultrasound sources using carbon-polymer nanocomposites for high frequency metrology
Srinath Rajagopal, Toby Sainsbury, Bradley E. Treeby, Ben T. Cox
The Journal of the Acoustical Society of America > Volume 144, Issue 2, pages 584-597, https://doi.org/10.1121/1.5048413


July 2018
Design of HIFU treatment plans using an evolutionary strategy
Marta Cudova, Bradley E Treeby, Jiří Jaroš
GECCO '18: Proceedings of the Genetic and Evolutionary Computation Conference CompanionJuly 2018, Pages 1568–1575, https://doi.org/10.1145/3205651.3208268


July 2018
GPU-Accelerated Simulation of Elastic Wave Propagation
K. Kadlubiak, J. Jaros and B. E. Treeby
International Conference on High Performance Computing & Simulation (HPCS), Orleans, 2018, pp. 188-195, https://doi.org/10.1109/HPCS.2018.00044


June 2018
Model-Based Learning for Accelerated, Limited-View 3-D Photoacoustic Tomography
Andreas Hauptmann, Felix Lucka, Marta Betcke, Nam Huynh, Jonas Adler, Ben Cox, Paul Beard, Sebastien Ourselin, Simon Arridge
IEEE Transactions on Medical Imaging, vol. 37, no. 6, pp. 1382-1393, DOI:10.1109/TMI.2018.2820382


2018
A framework for directional and higher-order reconstruction in photoacoustic tomography.
Boink, Y. E., Lagerwerf, M. J., Steenbergen, W., van Gils, S. A., Manohar, S., & Brune, C.
Physics in Medicine & Biology, 63(4), 045018; DOI:10.1088/1361-6560/aaaa4a


June 2018
A hierarchical Bayesian perspective on majorization-minimization for non-convex sparse regression: application to M/EEG source imaging
Yousra Bekhti, Felix Lucka, Joseph Salmon, Alexandre Gramfort
Inverse Problems, 34/8, DOI:10.1088/1361-6420/aac9b3


June 2018
Efficient Low-Resource Compression of HIFU Data.
Kleparnik Petr, Barina David, Zemcik Pavel and Jaros Jiri
Information. Basel: MDPI, 2018, vol. 9, no. 7, pp. 1-14. ISSN 2078-2489; DOI:10.3390/info9070155


February 2018
A framework for directional and higher-order reconstruction in photoacoustic tomography
Yoeri E Boink, Marinus J Lagerwerf, Wiendelt Steenbergen, Stephan A van Gils, Srirang Manohar, Christoph Brune
Physics in Medicine & Biology, 63/4, 045018, http://dx.doi.org/10.1088/1361-6560/aaaa4a


December 2017
Efficient Lossy Compression of Ultrasound Data.
Kleparnik Petr, Zemcik Pavel and Jaros Jiri
In: 2017 IEEE International Symposium on Signal Processing and Information Technology (ISSPIT). Bilbao: Institute of Electrical and Electronics Engineers, 2017, pp. 232-237. ISBN 978-1-5386-4662-5; DOI:10.1109/ISSPIT.2017.8388647


November 2017
Running Large-Scale Ultrasound Simulations on Piz Daint with 512 Pascal GPUs
Filip Vaverka; Bradley E. Treeby; Jiri Jaros
The International Conference for High Performance Computing, Networking, Storage and Analysis (Supercomputing 2017)


October 2017
Framework for Planning, Executing and Monitoring Cooperating Computations
Marta Cudova; Jiri Jaros
1st Users Conference of IT4Innovations, Ostrava


Prizes and Honors - PAMMOTH consortium


Best Research Poster Award at the International Supercomputing Conference in Frankfurt, Germany (https://www.isc-hpc.com/) for the poster by Kadlubiak Kristian, Jaros Jiri and Treeby Bradley E. GPU-accelerated Simulation of Elastic Wave Propagation. International Supercomputing Conference, Frankfurt am Main, 2018. ISC is the best European conference on high performance computing and usually ranked #2 in this area worldwide.


Excellent Poster Presentation Award - Signal Frequency Content and Appearance of Tumors in Photoacoustic Breast Tomography: A Simulation by Maura Dantuma, Felix Lucka, Bradley Treeby, Jiri Jaros, Ben Cox, and Srirang Manohar - Ultrasonics 2018, Caparica, Portugal.