GATE a GEANT4-based simulation toolkit for medical physics applications - IN2P3
←
→
Page content transcription
If your browser does not render page correctly, please read the page content below
GATE
Simulation of Preclinical andClinical Scans in Emission Tomography, Transmission Tomography and Radiation Therapy
FCPPL Workshop – Marseille, May 2018
GATE
a GEANT4-based simulation toolkit
for medical physics applications
supported by Uwe Pietrzyk, spokesperson of the
OpenGATE collaboration
What is GATE ?
www.opengatecollaboration.org
§ GATE: Geant4 Application for Emission Tomography,
Transmission Tomography, Radiotherapy and Optical Imaging
§ GATE is an Opensource software (GNU LGPL) dedicated to the
simulation of imaging (SPECT, PET, CT, Optical) and
radiotherapy, and based on the Geant4 toolbox
§ First release of GATE in May 2004
22 releases since that date
Currently GATE V8.1
§ Broad range of applications:
- Detector design
- Optimisation of acquisition and processing protocols
- Assessment of quantification methods
- Estimation of the system matrix used in tomographic
reconstruction
- Dosimetry, Radiation Therapy
- …
GATE 2004-2014: a constantly-upgraded platform
Acceleration
(2009) CT (2011)
Optical imaging
(2011) GPU (2014)
Planar
SPECT
PET (2004) Dosimetry Radiation therapy EduGATE (2011)
(2011) (2011) full energy
peak
(1600 keV) G4 DNA processes
(2014)
Double Single
escape peak escape peak
EduGATE - 2014 - U Pietrzyk / M Gaens - INM – FZ-Juelich / University of Wuppertal - Germany Slide 17
19 releases
2004 2011 2014 2017
1st GATE V6 GATE V7 GATE V8
GATE
IOP PUBLISHING PHYSICS IN MEDICINE AND BIOLOGY Journal of Biomedical Optics 19(2), 026004 (February 2014) TECHNISCHE MITTEILUNG
INSTITUTE OF PHYSICS PUBLISHING PHYSICS IN MEDICINE AND BIOLOGY Phys. Med. Biol. 56 (2011) 881–901 doi:10.1088/0031-9155/56/4/001
A review of the use and potential of the GATE Monte Carlo simulation code
for radiation therapy and dosimetry applications
Phys. Med. Biol. 49 (2004) 4543–4561 PII: S0031-9155(04)80763-2
Extension of the GATE Monte-Carlo simulation David Sarruta)
package to model bioluminescence and fluorescence
public
Université de Lyon, CREATIS; CNRS UMR5220; Inserm U1044; INSA-Lyon; Université Lyon 1;
Centre Léon Bérard, France
GATE V6: a major enhancement of the GATE
imaging Manuel Bardiès
GATE: a simulation toolkit for PET and SPECT simulation platform enabling modelling of CT and EduGATE – basic examples for educative purpose using the Inserm, UMR1037 CRCT, F-31000 Toulouse, France and Université Toulouse III-Paul Sabatier,
UMR1037 CRCT, F-31000 Toulouse, France
a b b a,
Vesna Cuplov, Iréne Buvat, Frédéric Pain, and Sébastien Jan *
GATE simulation platform
release
Nicolas Boussion
radiotherapy
a
Service Hospitalier Frédéric Joliot, Commissariat à l’Energie Atomique, 91401 Orsay, France
S Jan1, G Santin2,24 , D Strul2,25 , S Staelens3, K Assié4, D Autret5, b
Laboratoire Imagerie et Modélisation en Neurobiologie et Cancérologie, UMR 8165 CNRS—Université Paris 7—Université Paris 11, France INSERM, UMR 1101, LaTIM, CHU Morvan, 29609 Brest, France
S Avner6, R Barbier7, M Bardiès5, P M Bloomfield8, D Brasse6, Nicolas Freud
Uwe Pietrzyk 1,2,∗, Abdelhamid Zakhnini 2,3, Markus Axer 1,2, Sophie Sauerzapf 2,4, Didier Benoit 5, Michaela Gaens 1
V Breton9, P Bruyndonckx 10, I Buvat4, A F Chatziioannou11, Y Choi12, Abstract. The Geant4 Application for Emission Tomography (GATE) is an advanced open-source software Université de Lyon, CREATIS, CNRS UMR5220, Inserm U1044, INSA-Lyon, Université Lyon 1,
Y H Chung12, C Comtat1, D Donnarieix 9,13, L Ferrer5, S J Glick14, S Jan1 , D Benoit2 , E Becheva1 , T Carlier3,4 , F Cassol5 , P Descourt6 , dedicated to Monte-Carlo (MC) simulations in medical imaging involving photon transportation (Positron emis- 1
Institute of Neurosciences and Medicine (INM), Research Center Juelich, Germany Centre Léon Bérard, 69008 Lyon, France
C J Groiselle14, D Guez15, P-F Honore15, S Kerhoas-Cavata15, T Frisson7 , L Grevillot7 , L Guigues7 , L Maigne8 , C Morel5 , Y Perrot8 , sion tomography, single photon emission computed tomography, computed tomography) and in particle therapy. 2
Department of Mathematics and Natural Sciences, University of Wuppertal, Germany Sébastien Jan
In this work, we extend the GATE to support simulations of optical imaging, such as bioluminescence or fluo-
N Rehfeld2 , D Sarrut7 , D R Schaart9 , S Stute2 , U Pietrzyk10 , D Visvikis6 ,
3
HZDR - Resource Ecology, Research Site Leipzig, Germany
A S Kirov16, V Kohli11, M Koole3, M Krieguer10, D J van der Laan17, rescence imaging, and validate it against the MC for multilayered media standard simulation tool for biomedical 4
CEA/DSV/I2BM/SHFJ, Orsay 91401, France
Department of Nuclear Medicine, University Hospital Freiburg, Freiburg, Germany
F Lamare18, G Largeron7, C Lartizien19, D Lazaro9, M C Maas17, N Zahra7 and I Buvat2 optics in simple geometries. A full simulation set-up for molecular optical imaging (bioluminescence and fluo- 5 Jean-Michel Létang
Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC), Orsay, France
L Maigne9, F Mayet20, F Melot20, C Merheb15, E Pennacchio7, J Perez21, rescence) is implemented in GATE, and images of the light distribution emitted from a phantom demonstrate Université de Lyon, CREATIS, CNRS UMR5220, Inserm U1044, INSA-Lyon, Université Lyon 1,
1 DSV/I2BM/SHFJ, Commissariat à l’Energie Atomique, Orsay, France the relevance of using GATE for optical imaging simulations. © 2014 Society of Photo-Optical Instrumentation Engineers (SPIE) Centre Léon Bérard, 69008 Lyon, France
U Pietrzyk21, F R Rannou11,22, M Rey2, D R Schaart17, C R Schmidtlein16, 2 IMNC–UMR 8165 CNRS–Paris 7 and Paris 11 Universities, 15 rue Georges Clémenceau, [DOI: 10.1117/1.JBO.19.2.026004]
Received 3 April 2012; accepted 30 July 2012
L Simon2,26 , T Y Song12, J-M Vieira2, D Visvikis18, R Van de Walle3, 91406 Orsay Cedex, France George Loudos
Keywords: Monte-Carlo; simulation; bioluminescence; fluorescence. Department of Medical Instruments Technology, Technological Educational Institute of Athens,
E Wieërs10,23 and C Morel2 3 INSERM U892–Cancer Research Center, University of Nantes, Nantes, France
4 Nuclear Medicine Department, University Hospital of Nantes, Nantes, France Paper 130749R received Oct. 16, 2013; revised manuscript received Jan. 5, 2014; accepted for publication Jan. 7, 2014; published Abstract EduGATE – einfache lehrreiche Beispiele zum Athens 12210, Greece
online Feb. 12, 2014.
1 Service Hospitalier Frédéric Joliot (SHFJ), CEA, F-91401 Orsay, France 5 Centre de physique des particules de Marseille, CNRS-IN2P3 and Université de la Zweck der Ausbildung basierend auf der Lydia Maigne
2 LPHE, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland EduGATE is a collection of basic examples to introduce
3
Méditerranée, Aix-Marseille II, 163, avenue de Luminy, 13288 Marseille Cedex 09, France GATE Simulationsplattform UMR 6533 CNRS/IN2P3, Université Blaise Pascal, 63171 Aubière, France
ELIS, Ghent University, B-9000 Ghent, Belgium 6 INSERM, U650, Laboratoire du Traitement de l’Information Medicale (LaTIM), CHU Morvan,
1 Introduction techniques from cell resolution microscopy to full field noninva- students to the fundamental physical aspects of medical
4 INSERM U494, CHU Pitié-Salpêtrière, F-75634 Paris, France
Brest, France sive 3-D tomography.7 Preclinical imaging of bioluminescence imaging devices. It is based on the GATE platform, which Sara Marcatili and Thibault Mauxion
5 INSERM U601, CHU Nantes, F-44093 Nantes, France 7 Université de Lyon, CREATIS, CNRS UMR5220, Inserm U630, INSA-Lyon, Université Lyon Monte-Carlo (MC) simulations play an increasing role in has received a wide acceptance in the field of simulating Zusammenfassung Inserm, UMR1037 CRCT, F-31000 Toulouse, France and Université Toulouse III-Paul Sabatier,
or fluorescence signals from tagged cancerous cells in mouse
6 Institut de Recherches Subatomiques, CNRS/IN2P3 et Université Louis Pasteur,
1, Centre Léon Bérard, France medical imaging techniques involving radiations [positron medical imaging devices including SPECT, PET, CT and UMR1037 CRCT, F-31000 Toulouse, France
models has become a reference technique for rapid screening
F-67037 Strasbourg, France 8 Laboratoire de Physique Corpusculaire, 24 Avenue des Landais, 63177 Aubière Cedex, France emission tomography (PET), single photon emission computed EduGATE ist eine Sammlung einfacher basaler Beispiele
7 Institut de Physique Nucléaire de Lyon, CNRS/IN2P3 et Université Claude Bernard, of molecules with a potential therapeutic impact.8,9,10 also applications in radiation therapy. GATE can be con- Panagiotis Papadimitroulas
9 Delft University of Technology, Radiation Detection & Medical Imaging, Mekelweg 15, tomography (SPECT), and computed tomography (CT)]. für Studenten zur Einführung in die fundamentalen Aspekte
The MC modeling in light transport simulations11 is used to figured by commands, which are, for the sake of simplicity, Department of Biomedical Engineering, Technological Educational Institute of Athens, 12210, Athens, Greece
F-69622 Villeurbanne, France For these applications, simulations are used to help design der bildgebenden Systeme in der Medizin. Sie baut auf der
8 PET Group, Centre for Addiction and Mental Health, Toronto, Ontario M5T 1R8, Canada 2629 JB Delft, The Netherlands optimize imaging systems12 and data interpretation, to study the listed in a collection of one or more macro files to set up
10 Reseach Center Juelich, Institute of Neurosciences and Medicine and Department of Physics, and assess new imaging devices, and to optimize the acquisi- GATE-Plattform auf, die im Feld der Simulation bildgeben- Yann Perrot
9 Laboratoire de Physique Corpusculaire, CNRS/IN2P3, Université Blaise Pascal, optimal structural and optical properties of nanophosphors,13 or phantoms, multiple types of sources, detection device, and
University of Wuppertal, Germany tion and data processing protocols. The Geant4 Application der Systeme besonders SPECT, PET, CT, ebenso auch UMR 6533 CNRS/IN2P3, Université Blaise Pascal, 63171 Aubière, France
Campus des Cézeaux, F-63177 Aubière, France to simultaneously image two distinct fluorophores with lifetime acquisition parameters. The aim of the EduGATE is to use
for Emission Tomography (GATE)1,2 open-source simulation contrast.14 The MC software simulating the photon migration in Strahlentherapie eine weite Verbreitung gefunden hat.
10 Inter-University Institute for High Energies, Vrije Universiteit Brussel, B-1050 Brussel,
platform, based on the Geant4 toolkit,3,4 has been all these helpful features of GATE to provide insights into Uwe Pietrzyk
Belgium E-mail: buvat@imnc.in2p3.fr complex 3-D shapes, such as the tetrahedron-based inhomo- the physics of medical imaging by means of a collection GATE wird gewöhnlich durch Kommandos gesteuert, die Institut für Neurowissenschaften und Medizin, Forschungszentrum Jülich GmbH, 52425 Jülich,
developed since 2002 by the OpenGATE collaboration (www geneous MC optical simulator,15 the molecular optical simulation zur Vereinfachung in eine Reihe von Dateien (Makros)
11 Crump Institute for Molecular Imaging, University of California, Los Angeles,
of very basic and simple GATE macros in connection with Germany and Fachbereich für Mathematik und Naturwissenschaften, Bergische Universität Wuppertal,
.opengatecollaboration.org) and is currently widely used by environment,16 the mesh-based MC,17 and the MC for multilay- zusammengefasst sind und Phantome, verschiedene Typen
CA 90095-1770, USA Received 6 August 2010, in final form 29 November 2010 analysis programs based on ROOT, a framework for data 42097 Wuppertal, Germany
the research community involved in SPECT and PET molecular ered media (MCML),18 have been thoroughly described before.
12 Department of Nuclear Medicine, Samsung Medical Center, Sungkyunkwan University School
processing. A graphical user interface to define a configu- an Quellen, Nachweisdetektor und Akquisitionsparameter
Published 19 January 2011 imaging. Moreover, recently, the rise of optogenetics has As complex geometries were obtained at the expense of heavy beschreiben. Das Ziel, EduGATE zu entwickeln, war, diese Charlotte Robert
of Medicine, Seoul 135-710, Korea ration is also included.
13 Département de Curiethérapie-Radiothérapie, Centre Jean Perrin, F-63000 Clermont-Ferrand, Online at stacks.iop.org/PMB/56/881 opened the possibility to address and trigger action potentials calculations, in recent years extensive efforts were targeted at IMNC, UMR 8165 CNRS, Universités Paris 7 et Paris 11, Orsay 91406, France
vielfältigen, sehr nützlichen Eigenschaften zu nutzen, um
in specific cells with light.5 In these experimental paradigms, increasing the computational efficiency through parallelization
France mithilfe sehr einfacher GATE-Makros dem interessierten Dennis R. Schaart
14 University of Massachusetts Medical School, Division of Nuclear Medicine, Worcester, it is of a great interest to study the light path and fluence dis- using clusters or graphics processing unit (GPU) calculators.19,20
Abstract tribution in tissues, as the penetration depth and deposited power Nutzer Zugang zur Physik der medizinischen Bildgebung Delft University of Technology, Faculty of Applied Sciences, Radiation Science and Technology Department,
MA 01655, USA Recently, the GAMOS MC application has been upgraded to Delft Mekelweg 15, 2629 JB Delft, The Netherlands
GATE (Geant4 Application for Emission Tomography) is a Monte Carlo per millimeter will determine the spatial extension of cell acti- zu ermöglichen, verbunden mit einem Analyseprogramm
15 DAPNIA, CEA Saclay, F-91191 Gif-Sur-Yvette, France model the light transport due to Cerenkov effect.21 Yet, there
simulation platform developed by the OpenGATE collaboration since 2001 vation. Yet, only coarse experimental measurements and simpli- basierend auf ROOT, einem Softwarepaket für Datenana- Dimitris Visvikis
16 Department of Medical Physics, Memorial Sloan-Kettering Cancer Center, New York, is currently no MC code offering the same flexibility for model-
fied two-dimensional (2-D) modeling are currently used in this ing a wide range of experimental set-up as GATE does for nuclear lyse. Eine graphische Benutzerschnittstelle zur Definition INSERM U1101, LaTIM, CHU Morvan, 29609 Brest, France
NY 10021, USA and first publicly released in 2004. Dedicated to the modelling of planar der gewünschten Konfiguration ist eingeschlossen.
17 Delft University of Technology, IRI, Radiation Technology, 2629 JB Delft, rapidly growing field.6 The MC simulations might be a great imaging applications. Given that optical imaging is a matter of
The Netherlands
scintigraphy, single photon emission computed tomography (SPECT) and asset in that context. photon transportation, we present here an extension of GATE
Irène Buvat
positron emission tomography (PET) acquisitions, this platform is widely used Keywords: Monte Carlo Simulation, GATE, PET, Schlüsselwörter: Monte-Carlo-Simulation, GATE, PET, IMNC, UMR 8165 CNRS, Universités Paris 7 et Paris 11, 91406 Orsay, France and CEA/DSV/I2BM/SHFJ,
18 INSERM U650, Laboratoire de Traitement de l’Information Médicale (LATIM), In the last decade, optical imaging has become a major so that it can model optical imaging experiments, such as biolu- 91400 Orsay, France
CHU Morvan, F-29609 Brest, France to assist PET and SPECT research. A recent extension of this platform, released modality in the preclinical setting, especially for screening can- minescence or fluorescence imaging and validate it against the SPECT, Education, Imaging SPECT, Bildgebung, Ausbildung
19 ANIMAGE-CERMEP, Université Claude Bernard Lyon 1, F-69003 Lyon, France
by the OpenGATE collaboration as GATE V6, now also enables modelling of cerous models in mice. Although the transition from bench to MCML simulation tool. (Received 16 September 2013; revised 24 March 2014; accepted for publication 30 March 2014;
20 Laboratoire de Physique Subatomique et de Cosmologie, CNRS/IN2P3 et Université
bedside is yet to be achieved in most cases, there is an increasing The resulting extended version of GATE (GATE V6.2) there- published 12 May 2014)
Joseph Fourier, F-38026 Grenoble, France x-ray computed tomography and radiation therapy experiments. This paper interest for optical imaging of endogenous or exogenous probes. fore offers an original platform for bioluminescence and fluo-
presents an overview of the main additions and improvements implemented in These techniques are generally noninvasive, low cost and allow rescence imaging, including some unique features that are not In this paper, the authors’ review the applicability of the open-source GATE Monte Carlo simulation
currently offered by other codes: platform based on the GEANT4 toolkit for radiation therapy and dosimetry applications. The
GATE since the publication of the initial GATE paper (Jan et al 2004 Phys. for real time study of biological processes through three-dimes-
nional (3-D) images of the light distribution emitted from the ∗ Corresponding many applications of GATE for state-of-the-art radiotherapy simulations are described including
24 Present address: ESA—European Space and Technology Centre, 2200 AG Noordwijk, The Netherlands.
Med. Biol. 49 4543–61). This includes new models available in GATE • a user friendly implementation of material and surface
author: Prof. Dr. Uwe Pietrzyk, Institute of Neuroscience and Medicine, Research Center Juelich, 52425, Jülich, Germany.
external beam radiotherapy, brachytherapy, intraoperative radiotherapy, hadrontherapy, molecular
surface of small animals or superficial areas in humans. Optical E-mail: u.pietrzyk@fz-juelich.de (U. Pietrzyk).
25 Present address: CNRS-LESIA, Observatoire de Meudon, F-92190 Meudon, France. to simulate optical and hadronic processes, novelties in modelling tracer, imaging modalities encompass a rapidly growing range of properties using the extensible markup language (XML) radiotherapy, and in vivo dose monitoring. Investigations that have been performed using GEANT4
26 Present address: Institut Curie, Service de Physique Médicale, F-75005 Paris, France.
organ or detector motion, new options for speeding up GATE simulations, only are also mentioned to illustrate the potential of GATE. The very practical feature of GATE
examples illustrating the use of GATE V6 in radiotherapy applications and *Address all correspondence to: Sébastien Jan, E-mail: sebastien.jan@cea.fr 0091-3286/2014/$25.00 © 2014 SPIE making it easy to model both a treatment and an imaging acquisition within the same framework
0031-9155/04/194543+19$30.00 © 2004 IOP Publishing Ltd Printed in the UK 4543 Z. Med. Phys. 23 (2013) 65–70
http://dx.doi.org/10.1016/j.zemedi.2012.07.005
0031-9155/11/040881+21$33.00 © 2011 Institute of Physics and Engineering in Medicine Printed in the UK 881 064301-1 Med. Phys. 41 (6), June 2014 0094-2405/2014/41(6)/064301/14/$30.00 © 2014 Am. Assoc. Phys. Med. 064301-1
Journal of Biomedical Optics 026004-1 February 2014 • Vol. 19(2) http://journals.elsevier.de/zemedi
Main technical features of GATE (1) § GATE is based on Geant4: http://www.geant4.org § GATE is written in C++ § GATE is user-friendly as simulations can be designed and controlled using macros, without any C++ writing § GATE can simulate SPECT, PET, CT and optical scans and radiotherapy treatments § GATE is flexible enough to model almost any detector design, including prototypes § GATE explicitly models time, hence makes it possible to model detector motion, patient motion, radioactive decay, optical photon tracking, dead time, time of flight, tracer kinetics § GATE can handle analytical or voxelized phantoms § GATE can run on a cluster architecture and on a grid
Main technical features of GATE (2) § GATE can be freely downloaded, including sources § GATE can be run on many platforms (Linux, MAC OS, Windows) § Online documentation about GATE, including FAQ § Help about the use of GATE can be obtained through the gate-user mailing list (more than 1500 subscribers) § Many commercial or prototype systems have already been modeled using GATE and most models have been thoroughly validated (list available at the address: http://www.opengatecollaboration.org) § The GATE project is mostly based on volunteer participation and on the active contribution of GATE developers and users
The OpenGATE collaboration
§ 18 labs, sharing developments and validation studies regarding
GATE, and working together to make these developments
publicly available
France Europe
q U892 Inserm, Nantes q Delft University of Technology, Delft, The Netherlands
q LaTIM, U1101 Inserm, Brest q Forschungszentrum Juelich, Germany
q IMNC, CNRS/IN2P3, Orsay q National Technical University of Athens, Greece
q LPC, CNRS/IN2P3, Clermont-Fd q Medical University of Vienna, Austria
q IPHC, CNRS/IN2P3, Strasbourg q MedAustron, Wiener Neustadt, Austria
q CPPM, CNRS/IN2P3, Marseille q University of Gent, Belgium
q CREATIS, CNRS, Lyon
q SHFJ-CEA, Orsay
q U1037 Inserm, Toulouse
Rest of the world
q Memorial Sloan-Kettering Cancer Center, New York, USA
q UC Davis, Davis, USA
qSogang University, Seoul, South Korea
-> Need to foster collaborations with China
Research topics developed in IN2P3 labs
IMNC (Imaging & Thermotherapy) IPHC (Dosimetry and radiation protection)
Distribution of light within monolithic Dosimetry using scintillating fiber in radiology
scintillators (miniaturized Dosimetry for radiation protection in interventional
gamma camera) radiology
Variance reduction technique for the calculation of
dose using neutrons (nTLE)
Nuclear activation of materials irradiated with high
Study of optimal parameters for energy X-rays
photostimulation Dosimetry using CMOS detectors
in protontherapy
LPC Clermont (Dosimetry & Radiobiology) CPPM (Imaging)
Pre-clinical and clinical dosimetry for internal Compton camera:
radiation therapy (new theranostic molecules) Modelling of SiPM arrays
Performance study and
development of new
reconstruction algorithms
Evaluation of the biological dose in hadrontherapy
Radiobiology: evaluation of cell and DNA damage
µCT imaging:
Simulation of hybrid pixel detectors
Partnerships with chinese particle physics labs
u Foster research partnerships & enlarge the
OpenGATE collaboration to Chinese labs
GATE is now a powerful and recognized platform for medical
physics applications, but it needs to be maintained and
developed in the long term through research partnerships
(PhD thesis)
Partnerships with chinese particle physics labs
u Foster research partnerships & enlarge the
OpenGATE collaboration to Chinese labs
GATE is now a powerful and recognized platform for medical
physics applications, but it needs to be maintained and
developed in the long term through research partnerships
(PhD thesis)
u Foster education on simulation and
modelling in medical physics through
dedicated workshops and tutorials
• French students are trained to use GATE in medical physics
Master programs in order to help their understanding of
particle physics interactions and operation of medical
devices
• The OpenGATE collaboration is willing to develop dedicated
workshops to train Master students and open new
collaborations sall around the world -> FCPPL could help in
finding new partners
Contact & References Ø Contact: Lydia Maigne, associate professor @ LPC Clermont- Ferrand, Lydia.Maigne@clermont.in2p3.fr Ø References: Ø GATE URL: http://www.opengatecollaboration.org Ø GATE user mailing list: gate-users@lists.opengatecollaboration.org Ø GATE documentation (wiki): Ø To install GATE: http://www.opengatecollaboration.org/InstallingGATE Ø To use GATE: http://www.opengatecollaboration.org/Documentation Ø GATE publications: http://www.opengatecollaboration.org/Publications
You can also read
