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

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. (UPSY FIT VUT) , research leader
Bordovský Gabriel, Ing. (UPSY FIT VUT) , team leader
Budiský Jakub, Ing. (UPSY FIT VUT) , team leader
Čudová Marta, Ing. (UPSY FIT VUT) , team leader
Jaroš Marta, Ing., PhD. (UPSY FIT VUT) , team leader
Kadlubiak Kristián, Ing. (UPSY FIT VUT) , team leader
Vaverka Filip, Ing. (UPSY FIT VUT) , team leader

Publications

2021

PHAM Khoa, NOIMARK Sacha, HUYNH Nam, ZHANG Edward, KUKLIŠ Filip, JAROŠ Jiří, DESJARDINS Adrien, COX Ben T. and BEARD Paul. Broadband all-optical plane-wave ultrasound imaging system based on a Fabry-Perot scanner. IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, vol. 68, no. 4, 2021, pp. 1007-1016. ISSN 1525-8955. Detail
JAROŠ Marta, SASÁK Tomáš, TREEBY Bradley E. and JAROŠ Jiří. 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, pp. 116-134. ISBN 978-3-030-67076-4. Detail
VAVERKA Filip, TREEBY Bradley E. and JAROŠ Jiří. 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, pp. 99-115. ISBN 978-3-030-67076-4. Detail
JAROŠ Marta and JAROŠ Jiří. Performance-Cost Optimization of Moldable Scientific Workflows. In: Job Scheduling Strategies for Parallel Processing. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Portland, Oregon USA: Springer International Publishing, 2021, pp. 149-167. ISBN 978-3-030-88223-5. ISSN 0302-9743. Detail

2020

MARTIN Eleanor, JAROŠ Jiří and TREEBY Bradley E. Experimental Validation of k-Wave: Nonlinear Wave Propagation in Layered, Absorbing Fluid Media. IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, vol. 67, no. 1, 2020, pp. 81-91. ISSN 1525-8955. Detail
JAROŠ Marta, TREEBY Bradley E., GEORGIOU Panayiotis and JAROŠ Jiří. 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, pp. 1-10. ISBN 978-1-4503-7993-9. Detail
JAROŠ Marta, KLUSÁČEK Dalibor and JAROŠ Jiří. 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), vol. 12326. New Orleans: Springer Nature Switzerland AG, 2020, pp. 68-84. ISBN 978-3-030-63170-3. Detail

2019

JAROŠ Marta, TREEBY Bradley E. and JAROŠ Jiří. Adaptive Execution Planning in Biomedical Workflow Management Systems. Ostrava, 2019. Detail
JAROŠ Marta, JAROŠ Jiří and TREEBY Bradley E. Adaptive Execution Planning in Workflow Management Systems. Denver, 2019. Detail
VAVERKA Filip, TREEBY Bradley E. and JAROŠ Jiří. Advancements in Ultrasound Simulations Enabled by High-bandwidth GPU Interconnects. Denver, 2019. Detail
VAVERKA Filip, TREEBY Bradley E. and JAROŠ Jiří. 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, vol. 11538. Faro: Springer International Publishing, 2019, pp. 577-590. ISBN 978-3-030-22743-2. Detail
BORDOVSKÝ Gabriel and JAROŠ Jiří. On the Complexity of Photoacoustic Tomography: A Trade-off Between Image Quality and Computational Cost. Solaň, 2019. Detail
BORDOVSKÝ Gabriel. Photoacoustic Reconstruction with Progressive Grid Refinement. Ostrava, 2019. Detail
WISE Elliott S., COX Ben T., JAROŠ Jiří and TREEBY Bradley E. Representing arbitrary acoustic source and sensor distributions in Fourier collocation methods. Journal of the Acoustical Society of America, vol. 146, no. 1, 2019, pp. 278-288. ISSN 1520-8524. Detail
JAROŠ Marta, TREEBY Bradley E. and JAROŠ Jiří. Scientific workflow management framework. Soláň, 2019. Detail

2018

ČUDOVÁ Marta, TREEBY Bradley E. and JAROŠ Jiří. 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, pp. 1568-1575. ISBN 978-1-4503-5764-7. Detail
JAROŠ Marta, TREEBY Bradley E. and JAROŠ Jiří. Design of HIFU Treatment Plans using an Evolutionary Strategy. Ostrava, 2018. Detail
KLEPÁRNÍK Petr, ZEMČÍK Pavel and JAROŠ Jiří. 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, pp. 232-237. ISBN 978-1-5386-4662-5. Detail
KLEPÁRNÍK Petr, BAŘINA David, ZEMČÍK Pavel and JAROŠ Jiří. Efficient Low-Resource Compression of HIFU Data. Information, vol. 9, no. 7, 2018, pp. 1-14. ISSN 2078-2489. Detail
KADLUBIAK Kristián, TREEBY Bradley E. and JAROŠ Jiří. Fourth-order Time-stepping Scheme in Simulation of Ultrasound Propagation. Ostrava, 2018. Detail
KADLUBIAK Kristián, JAROŠ Jiří and TREEBY Bradley E. GPU-accelerated Simulation of Elastic Wave Propagation. Frankfurt am Main, 2018. Detail
KADLUBIAK Kristián, JAROŠ Jiří and TREEBY Bradley E. 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, pp. 188-195. ISBN 978-1-5386-7878-7. Detail
BORDOVSKÝ Gabriel. Challenges In the Computer Photoacoustic Tomograpy Using the k-Wave Toolbox. In: Počítačové architektúry & diagnostika PAD 2018. Plzeň: University of West Bohemia in Pilsen, 2018, pp. 49-52. ISBN 978-80-261-0814-6. Detail
VAVERKA Filip, ŠPEŤKO Matej, TREEBY Bradley E. and JAROŠ Jiří. Optimization of Ultrasound Simulations on Multi-GPU Servers. Dallas, 2018. Detail
TREEBY Bradley E., VAVERKA Filip and JAROŠ Jiří. Performance and Accuracy Analysis of Nonlinear k-Wave Simulations Using Local Domain Decomposition with an 8-GPU Server. Proceedings of Meetings on Acoustics, vol. 34, no. 1, 2018, pp. 1-5. ISSN 1939-800X. Detail
BORDOVSKÝ Gabriel, COX Ben T. and JAROŠ Jiří. Photoacoustic Tomography Using the k-Wave Toolbox. Ostrava, 2018. Detail
VAVERKA Filip, TREEBY Bradley E. and JAROŠ Jiří. Running Large-Scale Ultrasound Simulations on Intel Xeon Phi (KNC) accelerators. Ostrava, 2018. Detail
DANTUMA Maura, LUCKA Felix, TREEBY Bradley E., JAROŠ Jiří, COX Ben T. and MANOHAR Srirang. Signal Frequency Content and Appearance of Tumors in Photoacoustic Breast Tomography: A Simulation. Caparica, 2018. Detail

2017

ČUDOVÁ Marta and JAROŠ Jiří. Framework for Planning, Executing and Monitoring Cooperating Computations. Ostrava, 2017. Detail
JAROŠ Jiří. High Performance Computing in Ultrasound Cancer Treatment. Brno, 2017. Detail
VAVERKA Filip, TREEBY Bradley E. and JAROŠ Jiří. Running Large-Scale Ultrasound Simulations on 256 Salomon Nodes. Ostrava, 2017. Detail
VAVERKA Filip, TREEBY Bradley E. and JAROŠ Jiří. Running Large-Scale Ultrasound Simulations on Piz Daint with 512 Pascal GPUs. Denver, 2017. Detail
TREEBY Bradley E., BUDISKÝ Jakub, WISE Elliott S., JAROŠ Jiří and COX Ben T. Single-step Calculation of the Acoustic Field from Arbitrary Continuous-wave Sources. Ostrava, 2017. Detail

Products

2020

C++ implementation of acoustic field calculation in k-Wave 1.3, software, 2020
Authors: Budiský Jakub, Treeby Bradley E., Jaroš Jiří Detail
C++ implementation of the k-Wave Toolbox version 1.3, software, 2020
Authors: Jaroš Jiří, Treeby Bradley E., Cox Ben T., Kukliš Filip Detail
CUDA implementation of the k-Wave Toolbox version 1.3, software, 2020
Authors: Jaroš Jiří, Treeby Bradley E. Detail

2017

C++ implementation of the k-Wave Toolbox version 1.2, software, 2017
Authors: Jaroš Jiří, Treeby Bradley E., Cox Ben T. Detail
CUDA implementation of the k-Wave Toolbox version 1.2, software, 2017
Authors: Jaroš Jiří, Treeby Bradley E. Detail