Project detail

Photoacoustic/Ultrasound Mammoscopy for evaluating screening-detected lesions in the breast

Duration: 01.01.2017 — 30.06.2021

Funding resources

Ministerstvo školství, mládeže a tělovýchovy ČR - Společná technologická iniciativa ECSEL

- whole funder (2017-01-01 - 2021-06-30)

On the project

PAMMOTH's objective is to develop, validate and begin exploitation of a dedicated breast imaging device for a significant impact in breast cancer diagnosis. The proposed device combines non-invasive 3D photoacoustic imaging and laser-induced ultrasound imaging. The device will provide near real-time, full-breast, multimodal images to the radiologist. From the ultrasound mode, the radiologist will visualize anatomical features and extent of tumors, and from multiwavelength photoacoustics, she will see tumor vascularity. Quantitative spectroscopic photoacoustic images will be extracted off-line, providing the radiologist information relating to tumor physiology and function such as angiogenesis and hypoxia. The choice of the relevant biological targets, and of the functionalities and technical principles applied in the PAMMOTH imager, will enable sensitive, accurate and quantitative measurements of these targets. This will provide relevant information to the radiologist to make accurate diagnosis with high specificity. We aim to make the imaging device such for all populations of women, with short time intervals between positive screening and diagnosis, having high through-put, possessing no carcinogenic potential and causing no pain and discomfort to patients.

Description in Czech
Cílem projektu PAMMOTH je vyvinout, validovat a uvést do praxe nový přístroj pro neinvazivní screening prsou s cílem o včasnou diagnozu rakoviny prsou. Navržené zařízení kombinuje 3D fotoakustické snímkování a laserem indukované ultrazvukové snímkování. Cílem je dosáhnout vysoké přesnosti detekce v reálném čase.

Keywords
photoacoustic imaging, laser-induced ultrasound, high performance computing, numerical methods, breast cancer

Mark

PAMMOTH

Default language

English

People responsible

Jaroš Jiří, doc. Ing., Ph.D. - principal person responsible

Units

Department of Computer Systems
- co-beneficiary (2016-04-18 - 2021-06-30)
EKSPLA
- co-beneficiary (2016-04-18 - 2021-06-30)
Imasonic SAS
- co-beneficiary (2016-04-18 - 2021-06-30)
Medisch Spectrum Twente
- co-beneficiary (2016-04-18 - 2021-06-30)
PA Imaging Holding BV
- co-beneficiary (2016-04-18 - 2021-06-30)
tp21 GmbH
- co-beneficiary (2016-04-18 - 2021-06-30)
University College London
- co-beneficiary (2016-04-18 - 2021-06-30)
University of Bern
- co-beneficiary (2016-04-18 - 2021-06-30)
University of Twente
- beneficiary (2016-04-18 - 2021-06-30)

Results

KADLUBIAK, K.; JAROŠ, J.; TREEBY, B. GPU-accelerated Simulation of Elastic Wave Propagation. Frankfurt am Main: 2018. p. 0 (1 s.).
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VAVERKA, F.; TREEBY, B.; JAROŠ, J. Running Large-Scale Ultrasound Simulations on Intel Xeon Phi (KNC) accelerators. Ostrava: 2018. p. 1 (1 s.).
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JAROŠ, M.; TREEBY, B.; JAROŠ, J. Design of HIFU Treatment Plans using an Evolutionary Strategy. Ostrava: 2018. p. 1 (1 s.).
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KADLUBIAK, K.; TREEBY, B.; JAROŠ, J. Fourth-order Time-stepping Scheme in Simulation of Ultrasound Propagation. Ostrava: 2018. p. 1 (1 s.).
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BORDOVSKÝ, G. Challenges In the Computer Photoacoustic Tomograpy Using the k-Wave Toolbox. Počítačové architektúry & diagnostika PAD 2018. Plzeň: University of West Bohemia in Pilsen, 2018. p. 49-52. ISBN: 978-80-261-0814-6.
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TREEBY, B.; VAVERKA, F.; JAROŠ, J. Performance and Accuracy Analysis of Nonlinear k-Wave Simulations Using Local Domain Decomposition with an 8-GPU Server. Proceedings of Meetings on Acoustics, 2018, vol. 34, no. 1, p. 1-5. ISSN: 1939-800X.
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WISE, E.; COX, B.; JAROŠ, J.; TREEBY, B. Representing arbitrary acoustic source and sensor distributions in Fourier collocation methods. Journal of the Acoustical Society of America, 2019, vol. 146, no. 1, p. 278-288. ISSN: 1520-8524.
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VAVERKA, F.; TREEBY, B.; JAROŠ, J. Evaluation of the Suitability of Intel Xeon Phi Clusters for the Simulation of Ultrasound Wave Propagation using Pseudospectral Methods. In 19th International Conference on Computational Science 2019, Faro, Portugal, June 12-14, 2019. Lecture Notes in Computer Science. Faro: Springer International Publishing, 2019. p. 577-590. ISBN: 978-3-030-22743-2.
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MARTIN, E.; JAROŠ, J.; TREEBY, B. Experimental Validation of k-Wave: Nonlinear Wave Propagation in Layered, Absorbing Fluid Media. IEEE TRANSACTIONS ON ULTRASONICS FERROELECTRICS AND FREQUENCY CONTROL, 2020, vol. 67, no. 1, p. 81-91. ISSN: 1525-8955.
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JAROŠ, M.; TREEBY, B.; JAROŠ, J. Scientific workflow management framework. Soláň: 2019. p. 1 (1 s.).
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BORDOVSKÝ, G.; JAROŠ, J. On the Complexity of Photoacoustic Tomography: A Trade-off Between Image Quality and Computational Cost. Solaň: 2019. p. 1 (1 s.).
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KUKLIŠ, F.; TREEBY, B.; COX, B. Fast Reconstruction of Photoacoustic Images. Soláň: 2019. p. 1 (1 s.).
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JAROŠ, M.; JAROŠ, J.; TREEBY, B. Adaptive Execution Planning in Workflow Management Systems. Denver: 2019. p. 0-0.
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JAROŠ, M.; TREEBY, B.; JAROŠ, J. Adaptive Execution Planning in Biomedical Workflow Management Systems. Ostrava: 2019. p. 0-0.
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BORDOVSKÝ, G. Photoacoustic Reconstruction with Progressive Grid Refinement. Ostrava: 2019. p. 0-0.
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VAVERKA, F.; TREEBY, B.; JAROŠ, J. Advancements in Ultrasound Simulations Enabled by High-bandwidth GPU Interconnects. Denver: 2019. p. 0-0.
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JAROŠ, M.; TREEBY, B.; GEORGIOU, P.; JAROŠ, J. k-Dispatch: A Workflow Management System for the Automated Execution of Biomedical Ultrasound Simulations on Remote Computing Resources. In Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2020. New York: Association for Computing Machinery, 2020. p. 1-10. ISBN: 978-1-4503-7993-9.
Detail

JAROŠ, M.; JAROŠ, J. Performance-Cost Optimization of Moldable Scientific Workflows. In Job Scheduling Strategies for Parallel Processing. Lecture Notes in Computer Science. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Portland, Oregon USA: Springer International Publishing, 2021. p. 149-167. ISBN: 978-3-030-88223-5. ISSN: 0302-9743.
Detail

KADLUBIAK, K.; JAROŠ, J.; TREEBY, B. GPU-accelerated Simulation of Elastic Wave Propagation. In Proceedings - 2018 International Conference on High Performance Computing and Simulation, HPCS 2018. Orleans: IEEE Computer Society, 2018. p. 188-195. ISBN: 978-1-5386-7878-7.
Detail

JAROŠ, M.; TREEBY, B.; JAROŠ, J. Design of HIFU Treatment Plans using Evolutionary Strategy. In GECCO 2018 Companion - Proceedings of the 2018 Genetic and Evolutionary Computation Conference Companion. Kyoto: Association for Computing Machinery, 2018. p. 1568-1575. ISBN: 978-1-4503-5764-7.
Detail

JAROŠ, M.; SASÁK, T.; TREEBY, B.; JAROŠ, J. Estimation of Execution Parameters for k-Wave Simulations. In High Performance Computing in Science and Engineering. HPCSE 2019. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Cham: Springer Nature Switzerland AG, 2021. p. 116-134. ISBN: 978-3-030-67076-4.
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JAROŠ, M.; KLUSÁČEK, D.; JAROŠ, J. Optimizing Biomedical Ultrasound Workflow Scheduling Using Cluster Simulations. In Job Scheduling Strategies for Parallel Processing. JSSPP 2020. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). New Orleans: Springer Nature Switzerland AG, 2020. p. 68-84. ISBN: 978-3-030-63170-3.
Detail

PHAM, K.; NOIMARK, S.; HUYNH, N.; ZHANG, E.; KUKLIŠ, F.; JAROŠ, J.; DESJARDINS, A.; COX, B.; BEARD, P. Broadband all-optical plane-wave ultrasound imaging system based on a Fabry-Perot scanner. IEEE TRANSACTIONS ON ULTRASONICS FERROELECTRICS AND FREQUENCY CONTROL, 2021, vol. 68, no. 4, p. 1007-1016. ISSN: 1525-8955.
Detail

VAVERKA, F.; TREEBY, B.; JAROŠ, J. Performance Evaluation of Pseudospectral Ultrasound Simulations on a Cluster of Xeon Phi Accelerators. In High Performance Computing in Science and Engineering. HPCSE 2019. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Cham: Springer Nature Switzerland AG, 2021. p. 99-115. ISBN: 978-3-030-67076-4.
Detail

JAROŠ, J. High Performance Computing in Ultrasound Cancer Treatment. Brno: 2017. p. 0-0.
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VAVERKA, F.; TREEBY, B.; JAROŠ, J. Running Large-Scale Ultrasound Simulations on Piz Daint with 512 Pascal GPUs. Denver: 2017. p. 1 (1 s.).
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VAVERKA, F.; TREEBY, B.; JAROŠ, J. Running Large-Scale Ultrasound Simulations on 256 Salomon Nodes. Ostrava: 2017. p. 1 (1 s.).
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JAROŠ, M.; JAROŠ, J. Framework for Planning, Executing and Monitoring Cooperating Computations. Ostrava: 2017. p. 0-0.
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DANTUMA, M.; LUCKA, F.; TREEBY, B.; JAROŠ, J.; COX, B.; MANOHAR, S. Signal Frequency Content and Appearance of Tumors in Photoacoustic Breast Tomography: A Simulation. Caparica: 2018. p. 1 (1 s.).
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KADLUBIAK, K.; TREEBY, B.; JAROŠ, J. Simulation of Ultrasound Propagation in Bone. Ostrava: 2017. p. 1 (1 s.).
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BORDOVSKÝ, G.; COX, B.; JAROŠ, J. Photoacoustic Tomography Using the k-Wave Toolbox. Ostrava: 2018. p. 1 (1 s.).
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VAVERKA, F.; ŠPEŤKO, M.; TREEBY, B.; JAROŠ, J. Optimization of Ultrasound Simulations on Multi-GPU Servers. Dallas: 2018. p. 1-2.
Detail

BUDISKÝ, J.; TREEBY, B.; JAROŠ, J.: k-Wave-afp-omp-v1.3; C++ implementation of acoustic field calculation in k-Wave 1.3. http://www.k-wave.org/download.php. URL: http://www.k-wave.org/download.php. (software)
Detail

JAROŠ, J.; TREEBY, B.: k-Wave-fluid-cuda-v1.3; CUDA implementation of the k-Wave Toolbox version 1.3. http://www.k-wave.org. URL: http://www.k-wave.org. (software)
Detail

JAROŠ, J.; TREEBY, B.; KUKLIŠ, F.; COX, B.: k-Wave-fluid-omp-v1.3; C++ implementation of the k-Wave Toolbox version 1.3. http://www.k-wave.org. URL: http://www.k-wave.org. (software)
Detail

JAROŠ, J.; TREEBY, B.; COX, B.: k-Wave-fluid-omp-v1.2; C++ implementation of the k-Wave Toolbox version 1.2. http://www.k-wave.org. URL: http://www.k-wave.org. (software)
Detail

JAROŠ, J.; TREEBY, B.: k-Wave-fluid-cuda-v1.2; CUDA implementation of the k-Wave Toolbox version 1.2. http://www.k-wave.org. URL: http://www.k-wave.org. (software)
Detail

Link

https://www.pammoth-2020.eu

Responsibility: Jaroš Jiří, doc. Ing., Ph.D.