Project Details

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

Project Period: 1. 1. 2017 – 30. 6. 2021

Project Type: grant

Code: PAMMOTH

Agency: Ministerstvo školství, mládeže a tělovýchovy ČR

Program: Společná technologická iniciativa ECSEL

Czech title
Fotoakustická/ultrazvuková mamoskopie pro dektekci lézí v prsou
Type
grant
Keywords

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

Abstract

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.

Team members
Jaroš Jiří, doc. Ing., Ph.D. (DCSY) – research leader
Bordovský Gabriel, Ing.
Budiský Jakub, Ing.
Jaroš Marta, Ing., Ph.D. (DCSY)
Kadlubiak Kristián, Ing. (DCSY)
Vaverka Filip, Ing., Ph.D.
Publications

2021

  • 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
  • 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. 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

2020

  • 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
  • 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
  • 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. Detail

2019

  • BORDOVSKÝ, G. Photoacoustic Reconstruction with Progressive Grid Refinement. Ostrava: 2019. p. 0-0. Detail
  • 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.). Detail
  • JAROŠ, M.; JAROŠ, J.; TREEBY, B. Adaptive Execution Planning in Workflow Management Systems. Denver: 2019. p. 0-0. Detail
  • JAROŠ, M.; TREEBY, B.; JAROŠ, J. Adaptive Execution Planning in Biomedical Workflow Management Systems. Ostrava: 2019. p. 0-0. Detail
  • JAROŠ, M.; TREEBY, B.; JAROŠ, J. Scientific workflow management framework. Soláň: 2019. p. 1 (1 s.). Detail
  • KUKLIŠ, F.; TREEBY, B.; COX, B. Fast Reconstruction of Photoacoustic Images. Soláň: 2019. p. 1 (1 s.). Detail
  • VAVERKA, F.; TREEBY, B.; JAROŠ, J. Advancements in Ultrasound Simulations Enabled by High-bandwidth GPU Interconnects. Denver: 2019. p. 0-0. Detail
  • 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. Detail
  • 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. Detail

2018

  • 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. Detail
  • BORDOVSKÝ, G.; COX, B.; JAROŠ, J. Photoacoustic Tomography Using the k-Wave Toolbox. Ostrava: 2018. p. 1 (1 s.). Detail
  • 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.). Detail
  • JAROŠ, M.; TREEBY, B.; JAROŠ, J. Design of HIFU Treatment Plans using an Evolutionary Strategy. Ostrava: 2018. p. 1 (1 s.). 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
  • KADLUBIAK, K.; JAROŠ, J.; TREEBY, B. GPU-accelerated Simulation of Elastic Wave Propagation. Frankfurt am Main: 2018. p. 0 (1 s.). 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
  • KADLUBIAK, K.; TREEBY, B.; JAROŠ, J. Fourth-order Time-stepping Scheme in Simulation of Ultrasound Propagation. Ostrava: 2018. p. 1 (1 s.). Detail
  • KLEPÁRNÍK, P.; BAŘINA, D.; ZEMČÍK, P.; JAROŠ, J. Efficient Low-Resource Compression of HIFU Data. Information (Switzerland), 2018, vol. 9, no. 7, p. 1-14. ISSN: 2078-2489. Detail
  • KLEPÁRNÍK, P.; ZEMČÍK, P.; JAROŠ, J. Efficient Lossy Compression of Ultrasound Data. In 2017 IEEE International Symposium on Signal Processing and Information Technology, ISSPIT 2017. Bilbao: Institute of Electrical and Electronics Engineers, 2018. p. 232-237. ISBN: 978-1-5386-4662-5. Detail
  • 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. Detail
  • VAVERKA, F.; ŠPEŤKO, M.; TREEBY, B.; JAROŠ, J. Optimization of Ultrasound Simulations on Multi-GPU Servers. Dallas: 2018. p. 1-2. Detail
  • VAVERKA, F.; TREEBY, B.; JAROŠ, J. Running Large-Scale Ultrasound Simulations on Intel Xeon Phi (KNC) accelerators. Ostrava: 2018. p. 1 (1 s.). Detail

2017

  • JAROŠ, J. High Performance Computing in Ultrasound Cancer Treatment. Brno: 2017. p. 0-0. Detail
  • JAROŠ, M.; JAROŠ, J. Framework for Planning, Executing and Monitoring Cooperating Computations. Ostrava: 2017. p. 0-0. Detail
  • KADLUBIAK, K.; TREEBY, B.; JAROŠ, J. Simulation of Ultrasound Propagation in Bone. Ostrava: 2017. p. 1 (1 s.). Detail
  • TREEBY, B.; BUDISKÝ, J.; WISE, E.; JAROŠ, J.; COX, B. Single-step Calculation of the Acoustic Field from Arbitrary Continuous-wave Sources. Ostrava: 2017. p. 1 (1 s.). Detail
  • VAVERKA, F.; TREEBY, B.; JAROŠ, J. Running Large-Scale Ultrasound Simulations on 256 Salomon Nodes. Ostrava: 2017. p. 1 (1 s.). Detail
  • VAVERKA, F.; TREEBY, B.; JAROŠ, J. Running Large-Scale Ultrasound Simulations on Piz Daint with 512 Pascal GPUs. Denver: 2017. p. 1 (1 s.). Detail
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