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Sarrut D, Arbor N, Baudier T, Borys D, Etxebeste A, Fuchs H, Gajewski J, Grevillot L, Jan S, Kagadis GC, Kang HG, Kirov A, Kochebina O, Krzemien W, Lomax A, Papadimitroulas P, Pommranz C, Roncali E, Rucinski A, Winterhalter C, Maigne L. The OpenGATE ecosystem for Monte Carlo simulation in medical physics. Phys Med Biol 2022; 67:10.1088/1361-6560/ac8c83. [PMID: 36001985 PMCID: PMC11149651 DOI: 10.1088/1361-6560/ac8c83] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/24/2022] [Indexed: 11/12/2022]
Abstract
This paper reviews the ecosystem of GATE, an open-source Monte Carlo toolkit for medical physics. Based on the shoulders of Geant4, the principal modules (geometry, physics, scorers) are described with brief descriptions of some key concepts (Volume, Actors, Digitizer). The main source code repositories are detailed together with the automated compilation and tests processes (Continuous Integration). We then described how the OpenGATE collaboration managed the collaborative development of about one hundred developers during almost 20 years. The impact of GATE on medical physics and cancer research is then summarized, and examples of a few key applications are given. Finally, future development perspectives are indicated.
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Affiliation(s)
- David Sarrut
- Université de Lyon; CREATIS; CNRS UMR5220; Inserm U1294; INSA-Lyon; Université Lyon 1, Léon Bérard cancer center, Lyon, France
| | - Nicolas Arbor
- Université de Strasbourg, IPHC, CNRS, UMR7178, F-67037 Strasbourg, France
| | - Thomas Baudier
- Université de Lyon; CREATIS; CNRS UMR5220; Inserm U1294; INSA-Lyon; Université Lyon 1, Léon Bérard cancer center, Lyon, France
| | - Damian Borys
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Ane Etxebeste
- Université de Lyon; CREATIS; CNRS UMR5220; Inserm U1294; INSA-Lyon; Université Lyon 1, Léon Bérard cancer center, Lyon, France
| | - Hermann Fuchs
- MedAustron Ion Therapy Center, Wiener Neustadt, Austria
- Medical University of Vienna, Department of Radiation Oncology, Vienna, Vienna, Währinger Gürtel 18-20, A-1090 Wien, Austria
| | - Jan Gajewski
- Institute of Nuclear Physics Polish Academy of Sciences, Krakow, Poland
| | | | - Sébastien Jan
- Université Paris-Saclay, Inserm, CNRS, CEA, Laboratoire d'Imagerie Biomédicale Multimodale (BioMaps), F-91401 Orsay, France
| | - George C Kagadis
- 3DMI Research Group, Department of Medical Physics, School of Medicine, University of Patras, Patras, Greece
| | - Han Gyu Kang
- National Institutes for Quantum Science and Technology (QST), 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Assen Kirov
- Memorial Sloan Kettering Cancer, New York, NY 10021, United States of America
| | - Olga Kochebina
- Université Paris-Saclay, Inserm, CNRS, CEA, Laboratoire d'Imagerie Biomédicale Multimodale (BioMaps), F-91401 Orsay, France
| | - Wojciech Krzemien
- High Energy Physics Division, National Centre for Nuclear Research, Otwock-Świerk, Poland
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, S. Lojasiewicza 11, 30-348 Krakow, Poland
- Centre for Theranostics, Jagiellonian University, Kopernika 40 St, 31 501 Krakow, Poland
| | - Antony Lomax
- Center for Proton Therapy, PSI, Switzerland
- Department of Physics, ETH Zurich, Switzerland
| | | | - Christian Pommranz
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University Tuebingen, Roentgenweg 13, D-72076 Tuebingen, Germany
- Institute for Astronomy and Astrophysics, Eberhard Karls University Tuebingen, Sand 1, D-72076 Tuebingen, Germany
| | - Emilie Roncali
- University of California Davis, Departments of Biomedical Engineering and Radiology, Davis, CA 95616, United States of America
| | - Antoni Rucinski
- Institute of Nuclear Physics Polish Academy of Sciences, Krakow, Poland
| | - Carla Winterhalter
- Center for Proton Therapy, PSI, Switzerland
- Department of Physics, ETH Zurich, Switzerland
| | - Lydia Maigne
- Université Clermont Auvergne, Laboratoire de Physique de Clermont, CNRS, UMR 6533, F-63178 Aubière, France
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Michelet C, Li Z, Yang W, Incerti S, Desbarats P, Giovannelli JF, Barberet P, Delville MH, Gordillo N, Devès G, Seznec H. A Geant4 simulation for three-dimensional proton imaging of microscopic samples. Phys Med 2019; 65:172-180. [PMID: 31494371 DOI: 10.1016/j.ejmp.2019.08.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 08/29/2019] [Accepted: 08/29/2019] [Indexed: 11/18/2022] Open
Abstract
Proton imaging can be carried out on microscopic samples by focusing the beam to a diameter ranging from a few micrometers down to a few tens of nanometers, depending on the required beam intensity and spatial resolution. Three-dimensional (3D) imaging by tomography is obtained from proton transmission (STIM: Scanning Transmission Ion Microscopy) and/or X-ray emission (PIXE: Particle Induced X-ray Emission). In these experiments, the samples are dehydrated for under vacuum analysis. In situ quantification of nanoparticles has been carried out at CENBG in the frame of nanotoxicology studies, on cells and small organisms used as biological models, especially on Caenorhabditis elegans (C. elegans) nematodes. Tomography experiments reveal the distribution of mass density and chemical content (in g.cm-3) within the analyzed volume. These density values are obtained using an inversion algorithm. To investigate the effect of this data reduction process, we defined different numerical phantoms, including a (dehydrated) C. elegans phantom whose geometry and density were derived from experimental data. A Monte Carlo simulation based on the Geant4 toolkit was developed. Using different simulation and reconstruction conditions, we compared the resulting tomographic images to the initial numerical reference phantom. A study of the relative error between the reconstructed and the reference images lead to the result that 20 protons per shot can be considered as an optimal number for 3D STIM imaging. Preliminary results for PIXE tomography are also presented, showing the interest of such numerical phantoms to produce reference data for future studies on X-ray signal attenuation in thick samples.
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Affiliation(s)
- Claire Michelet
- CENBG, UMR5797, Université de Bordeaux, CNRS, F-33170 Gradignan, France.
| | - Zhuxin Li
- CENBG, UMR5797, Université de Bordeaux, CNRS, F-33170 Gradignan, France
| | - Wen Yang
- CENBG, UMR5797, Université de Bordeaux, CNRS, F-33170 Gradignan, France
| | - Sébastien Incerti
- CENBG, UMR5797, Université de Bordeaux, CNRS, F-33170 Gradignan, France.
| | - Pascal Desbarats
- Laboratoire Bordelais de Recherche en Informatique (LaBRI, UMR5800) Univ. Bordeaux, 351 Cours de la Libération, F-33405 Talence cedex, France.
| | | | - Philippe Barberet
- CENBG, UMR5797, Université de Bordeaux, CNRS, F-33170 Gradignan, France.
| | - Marie-Hélène Delville
- CNRS, Univ. Bordeaux, ICMCB, UMR5026, 87 avenue du Dr. A. Schweitzer, Pessac F-33608, France.
| | - Nuria Gordillo
- CENBG, UMR5797, Université de Bordeaux, CNRS, F-33170 Gradignan, France
| | - Guillaume Devès
- CENBG, UMR5797, Université de Bordeaux, CNRS, F-33170 Gradignan, France.
| | - Hervé Seznec
- CENBG, UMR5797, Université de Bordeaux, CNRS, F-33170 Gradignan, France.
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