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Author Borys, D. et al; Brzezinski, K.
Title ProTheRaMon-a GATE simulation framework for proton therapy range monitoring using PET imaging Type Journal Article
Year 2022 Publication Physics in Medicine and Biology Abbreviated Journal Phys. Med. Biol.
Volume 67 Issue 22 Pages 224002 - 15pp
Keywords proton therapy; GATE; Monte Carlo simulations; J-PET; medical imaging
Abstract Objective. This paper reports on the implementation and shows examples of the use of the ProTheRaMon framework for simulating the delivery of proton therapy treatment plans and range monitoring using positron emission tomography (PET). ProTheRaMon offers complete processing of proton therapy treatment plans, patient CT geometries, and intra-treatment PET imaging, taking into account therapy and imaging coordinate systems and activity decay during the PET imaging protocol specific to a given proton therapy facility. We present the ProTheRaMon framework and illustrate its potential use case and data processing steps for a patient treated at the Cyclotron Centre Bronowice (CCB) proton therapy center in Krakow, Poland. Approach. The ProTheRaMon framework is based on GATE Monte Carlo software, the CASToR reconstruction package and in-house developed Python and bash scripts. The framework consists of five separated simulation and data processing steps, that can be further optimized according to the user's needs and specific settings of a given proton therapy facility and PET scanner design. Main results. ProTheRaMon is presented using example data from a patient treated at CCB and the J-PET scanner to demonstrate the application of the framework for proton therapy range monitoring. The output of each simulation and data processing stage is described and visualized. Significance. We demonstrate that the ProTheRaMon simulation platform is a high-performance tool, capable of running on a computational cluster and suitable for multi-parameter studies, with databases consisting of large number of patients, as well as different PET scanner geometries and settings for range monitoring in a clinical environment. Due to its modular structure, the ProTheRaMon framework can be adjusted for different proton therapy centers and/or different PET detector geometries. It is available to the community via github (Borys et al 2022).
Address [Borys, Damian] Silesian Tech Univ, Dept Syst Biol & Engn, Gliwice, Poland, Email: damin.borys@polsl.pl
Corporate Author Thesis
Publisher IOP Publishing Ltd Place of Publication Editor
Language English Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (up) 0031-9155 ISBN Medium
Area Expedition Conference
Notes WOS:000885248200001 Approved no
Is ISI yes International Collaboration no
Call Number IFIC @ pastor @ Serial 5416
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Author Borja-Lloret, M.; Barrientos, L.; Bernabeu, J.; Lacasta, C.; Muñoz, E.; Ros, A.; Roser, J.; Viegas, R.; Llosa, G.
Title Influence of the background in Compton camera images for proton therapy treatment monitoring Type Journal Article
Year 2023 Publication Physics in Medicine and Biology Abbreviated Journal Phys. Med. Biol.
Volume 68 Issue 14 Pages 144001 - 16pp
Keywords Compton imaging; Compton camera; proton therapy; treatment monitoring; Monte Carlo simulation; image reconstruction; background
Abstract Objective. Background events are one of the most relevant contributions to image degradation in Compton camera imaging for hadron therapy treatment monitoring. A study of the background and its contribution to image degradation is important to define future strategies to reduce the background in the system. Approach. In this simulation study, the percentage of different kinds of events and their contribution to the reconstructed image in a two-layer Compton camera have been evaluated. To this end, GATE v8.2 simulations of a proton beam impinging on a PMMA phantom have been carried out, for different proton beam energies and at different beam intensities. Main results. For a simulated Compton camera made of Lanthanum (III) Bromide monolithic crystals, coincidences caused by neutrons arriving from the phantom are the most common type of background produced by secondary radiations in the Compton camera, causing between 13% and 33% of the detected coincidences, depending on the beam energy. Results also show that random coincidences are a significant cause of image degradation at high beam intensities, and their influence in the reconstructed images is studied for values of the time coincidence windows from 500 ps to 100 ns. Significance. Results indicate the timing capabilities required to retrieve the fall-off position with good precision. Still, the noise observed in the image when no randoms are considered make us consider further background rejection methods.
Address [Borja-Lloret, M.; Barrientos, L.; Bernabeu, J.; Lacasta, C.; Munoz, E.; Ros, A.; Roser, J.; Viegas, R.; Llosa, G.] Inst Fis Corpuscular IFIC, CSIC UV, Valencia, Spain, Email: Marina.Borja@csic.es
Corporate Author Thesis
Publisher IOP Publishing Ltd Place of Publication Editor
Language English Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (up) 0031-9155 ISBN Medium
Area Expedition Conference
Notes WOS:001022671300001 Approved no
Is ISI yes International Collaboration no
Call Number IFIC @ pastor @ Serial 5571
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Author de los Rios, M.; Petac, M.; Zaldivar, B.; Bonaventura, N.R.; Calore, F.; Iocco, F.
Title Determining the dark matter distribution in simulated galaxies with deep learning Type Journal Article
Year 2023 Publication Monthly Notices of the Royal Astronomical Society Abbreviated Journal Mon. Not. Roy. Astron. Soc.
Volume 525 Issue 4 Pages 6015-6035
Keywords methods: data analysis; software: simulations; galaxies: general; galaxies: haloes; dark matter
Abstract We present a novel method of inferring the dark matter (DM) content and spatial distribution within galaxies, using convolutional neural networks (CNNs) trained within state-of-the-art hydrodynamical simulations (Illustris-TNG100). Within the controlled environment of the simulation, the framework we have developed is capable of inferring the DM mass distribution within galaxies of mass similar to 10(11)-10(13)M(circle dot) from the gravitationally baryon-dominated internal regions to the DM-rich, baryon-depleted outskirts of the galaxies, with a mean absolute error always below approximate to 0.25 when using photometrical and spectroscopic information. With respect to traditional methods, the one presented here also possesses the advantages of not relying on a pre-assigned shape for the DM distribution, to be applicable to galaxies not necessarily in isolation, and to perform very well even in the absence of spectroscopic observations.
Address [de los Rios, Martin] Univ Estadual Paulista, ICTP South Amer Inst Fundamental Res, Inst Fis Teor, BR-01140070 Sao Paulo, SP, Brazil, Email: fabio.iocco.astro@gmail.com
Corporate Author Thesis
Publisher Oxford Univ Press Place of Publication Editor
Language English Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (up) 0035-8711 ISBN Medium
Area Expedition Conference
Notes WOS:001072112100006 Approved no
Is ISI yes International Collaboration yes
Call Number IFIC @ pastor @ Serial 5707
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Author Villaescusa-Navarro, F. et al; Villanueva-Domingo, P.
Title The CAMELS Project: Public Data Release Type Journal Article
Year 2023 Publication Astrophysical Journal Supplement Series Abbreviated Journal Astrophys. J. Suppl. Ser.
Volume 265 Issue 2 Pages 54 - 14pp
Keywords Cosmology; Hydrodynamical simulations; Astrostatistics; Galaxy formation
Abstract The Cosmology and Astrophysics with Machine Learning Simulations (CAMELS) project was developed to combine cosmology with astrophysics through thousands of cosmological hydrodynamic simulations and machine learning. CAMELS contains 4233 cosmological simulations, 2049 N-body simulations, and 2184 state-of-the-art hydrodynamic simulations that sample a vast volume in parameter space. In this paper, we present the CAMELS public data release, describing the characteristics of the CAMELS simulations and a variety of data products generated from them, including halo, subhalo, galaxy, and void catalogs, power spectra, bispectra, Lya spectra, probability distribution functions, halo radial profiles, and X-rays photon lists. We also release over 1000 catalogs that contain billions of galaxies from CAMELS-SAM: a large collection of N-body simulations that have been combined with the Santa Cruz semianalytic model. We release all the data, comprising more than 350 terabytes and containing 143,922 snapshots, millions of halos, galaxies, and summary statistics. We provide further technical details on how to access, download, read, and process the data at .
Address [Villaescusa-Navarro, Francisco; Genel, Shy; Angles-Alcazar, Daniel; Hassan, Sultan; Pisani, Alice; Wong, Kaze W. K.; Coulton, William R.; Steinwandel, Ulrich P.; Spergel, David N.; Burkhart, Blakesley; Wandelt, Benjamin; Somerville, Rachel S.; Bryan, Greg L.; Li, Yin] Flatiron Inst, Ctr Computat Astrophys, 162 5th Ave, New York, NY 10010 USA, Email: camel.simulations@gmail.com
Corporate Author Thesis
Publisher IOP Publishing Ltd Place of Publication Editor
Language English Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (up) 0067-0049 ISBN Medium
Area Expedition Conference
Notes WOS:000964876300001 Approved no
Is ISI yes International Collaboration yes
Call Number IFIC @ pastor @ Serial 5525
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Author Aguiar, P.; Rafecas, M.; Ortuño, J.E.; Kontaxakis, G.; Santos, A.; Pavia, J.; Rosetti, M.
Title Geometrical and Monte Carlo projectors in 3D PET reconstruction Type Journal Article
Year 2010 Publication Medical Physics Abbreviated Journal Med. Phys.
Volume 37 Issue 11 Pages 5691-5702
Keywords 3D PET; iterative reconstruction; list-mode reconstruction; ray-tracing techniques; Monte Carlo simulation; system response matrix
Abstract Purpose: In the present work, the authors compare geometrical and Monte Carlo projectors in detail. The geometrical projectors considered were the conventional geometrical Siddon ray-tracer (S-RT) and the orthogonal distance-based ray-tracer (OD-RT), based on computing the orthogonal distance from the center of image voxel to the line-of-response. A comparison of these geometrical projectors was performed using different point spread function (PSF) models. The Monte Carlo-based method under consideration involves an extensive model of the system response matrix based on Monte Carlo simulations and is computed off-line and stored on disk. Methods: Comparisons were performed using simulated and experimental data of the commercial small animal PET scanner rPET. Results: The results demonstrate that the orthogonal distance-based ray-tracer and Siddon ray-tracer using PSF image-space convolutions yield better images in terms of contrast and spatial resolution than those obtained after using the conventional method and the multiray-based S-RT. Furthermore, the Monte Carlo-based method yields slight improvements in terms of contrast and spatial resolution with respect to these geometrical projectors. Conclusions: The orthogonal distance-based ray-tracer and Siddon ray-tracer using PSF image-space convolutions represent satisfactory alternatives to factorizing the system matrix or to the conventional on-the-fly ray-tracing methods for list-mode reconstruction, where an extensive modeling based on Monte Carlo simulations is unfeasible.
Address [Aguiar, Pablo] Univ Santiago de Compostela, Dept Fis Particulas, Complexo Hosp Univ Santiago de Compostela, Fdn IDICHUS IDIS, Santiago De Compostela, Spain, Email: pablo.aguiar.fernandez@sergas.es
Corporate Author Thesis
Publisher Amer Assoc Physicists Medicine Amer Inst Physics Place of Publication Editor
Language English Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (up) 0094-2405 ISBN Medium
Area Expedition Conference
Notes ISI:000283747600015 Approved no
Is ISI yes International Collaboration no
Call Number IFIC @ elepoucu @ Serial 338
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Author ATLAS Collaboration (Adragna, P. et al); Castelo, J.; Castillo Gimenez, V.; Cuenca, C.; Ferrer, A.; Fullana, E.; Gonzalez, V.; Higon-Rodriguez, E.; Poveda, J.; Ruiz, A.; Salvachua, B.; Sanchis, E.; Solans, C.; Torres, J.; Valero, A.; Valls Ferrer, J.A.
Title Measurement of pion and proton response and longitudinal shower profiles up to 20 nuclear interaction lengths with the ATLAS Tile calorimeter Type Journal Article
Year 2010 Publication Nuclear Instruments & Methods in Physics Research A Abbreviated Journal Nucl. Instrum. Methods Phys. Res. A
Volume 615 Issue 2 Pages 158-181
Keywords Calorimeter; Test-beam; ATLAS; Monte Carlo simulation; GEANT4; Hadronic shower development; Pion-proton response; Longitudinal shower profile for hadrons
Abstract The response of pions and protons in the energy range of 20-180 GeV, produced at CERN's SPS H8 test-beam line in the ATLAS iron-scintillator Tile hadron calorimeter, has been measured. The test-beam configuration allowed the measurement of the longitudinal shower development for pions and protons up to 20 nuclear interaction lengths. It was found that pions penetrate deeper in the calorimeter than protons. However, protons induce showers that are wider laterally to the direction of the impinging particle. Including the measured total energy response, the pion-to-proton energy ratio and the resolution, all observations are consistent with a higher electromagnetic energy fraction in pion-induced showers. The data are compared with GEANT4 simulations using several hadronic physics lists. The measured longitudinal shower profiles are described by an analytical shower parametrization within an accuracy of 5-10%. The amount of energy leaking out behind the calorimeter is determined and parametrized as a function of the beam energy and the calorimeter depth. This allows for a leakage correction of test-beam results in the standard projective geometry.
Address [Hakobyan, H.; Simonyan, M.] Yerevan Phys Inst, Yerevan 375036, Armenia, Email: Margar.Simonyan@cern.ch
Corporate Author Thesis
Publisher Elsevier Science Bv Place of Publication Editor
Language English Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (up) 0168-9002 ISBN Medium
Area Expedition Conference
Notes ISI:000276299900002 Approved no
Is ISI yes International Collaboration yes
Call Number IFIC @ pastor @ Serial 252
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Author ATLAS Collaboration (Abat, E. et al); Castillo Gimenez, V.; Ferrer, A.; Gonzalez, V.; Higon-Rodriguez, E.; Mitsou, V.A.; Ruiz, A.; Sanchis, E.; Solans, C.; Torres, J.; Valero, A.; Valls Ferrer, J.A.
Title Study of energy response and resolution of the ATLAS barrel calorimeter to hadrons of energies from 20 to 350 GeV Type Journal Article
Year 2010 Publication Nuclear Instruments & Methods in Physics Research A Abbreviated Journal Nucl. Instrum. Methods Phys. Res. A
Volume 621 Issue 1-3 Pages 134-150
Keywords ATLAS; Calorimetry; Test-beam; Calibration; Simulation
Abstract A fully instrumented slice of the ATLAS detector was exposed to test beams from the SPS (Super Proton Synchrotron) at CERN in 2004. In this paper, the results of the measurements of the response of the barrel calorimeter to hadrons with energies in the range 20-350 GeV and beam impact points and angles corresponding to pseudo-rapidity values in the range 0.2-0.65 are reported. The results are compared to the predictions of a simulation program using the Geant 4 toolkit.
Address [Abata, E.; Arik, E.; Cetin, S. A.] Bogazici Univ, Fac Sci, Dept Phys, TR-80815 Bebek, Turkey, Email: atlassecretariat@cern.ch
Corporate Author Thesis
Publisher Elsevier Science Bv Place of Publication Editor
Language English Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (up) 0168-9002 ISBN Medium
Area Expedition Conference
Notes ISI:000281109100019 Approved no
Is ISI yes International Collaboration yes
Call Number IFIC @ elepoucu @ Serial 389
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Author AGATA Collaboration (Soderstrom, P.A. et al); Gadea, A.
Title Interaction position resolution simulations and in-beam measurements of the AGATA HPGe detectors Type Journal Article
Year 2011 Publication Nuclear Instruments & Methods in Physics Research A Abbreviated Journal Nucl. Instrum. Methods Phys. Res. A
Volume 638 Issue 1 Pages 96-109
Keywords gamma-ray tracking; AGATA; Monte Carlo simulations; HPGe detectors; Fusion-evaporation reactions
Abstract The interaction position resolution of the segmented HPGe detectors of an AGATA triple cluster detector has been studied through Monte Carlo simulations and in an in-beam experiment. A new method based on measuring the energy resolution of Doppler-corrected gamma-ray spectra at two different target to detector distances is described. This gives the two-dimensional position resolution in the plane perpendicular to the direction of the emitted gamma-ray. The gamma-ray tracking was used to determine the full energy of the gamma-rays and the first interaction point, which is needed for the Doppler correction. Five different heavy-ion induced fusion-evaporation reactions and a reference reaction were selected for the simulations. The results of the simulations show that the method works very well and gives a systematic deviation of <1 mm in the FVVHM of the interaction position resolution for the gamma-ray energy range from 60 keV to 5 MeV. The method was tested with real data from an in-beam measurement using a (30)5i beam at 64 MeV on a thin C-12 target. Pulse-shape analysis of the digitized detector waveforms and gamma-ray tracking was performed to determine the position of the first interaction point, which was used for the Doppler corrections. Results of the dependency of the interaction position resolution on the gamma-ray energy and on the energy, axial location and type of the first interaction point, are presented. The FVVHM of the interaction position resolution varies roughly linearly as a function of gamma-ray energy from 8.5 mm at 250 key to 4 mm at 1.5 MeV, and has an approximately constant value of about 4 mm in the gamma-ray energy range from 1.5 to 4 MeV.
Address [Soderstrom, P. -A.; Nyberg, J.; Al-Adili, A.; Atac, A.; Veyssiere, C.] Uppsala Univ, Dept Phys & Astron, SE-75121 Uppsala, Sweden, Email: P-A.Soderstrom@physics.uu.se
Corporate Author Thesis
Publisher Elsevier Science Bv Place of Publication Editor
Language English Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (up) 0168-9002 ISBN Medium
Area Expedition Conference
Notes ISI:000290082600015 Approved no
Is ISI yes International Collaboration yes
Call Number IFIC @ pastor @ Serial 619
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Author Pierre Auger Collaboration (Abreu, P. et al); Pastor, S.
Title Advanced functionality for radio analysis in the Offline software framework of the Pierre Auger Observatory Type Journal Article
Year 2011 Publication Nuclear Instruments & Methods in Physics Research A Abbreviated Journal Nucl. Instrum. Methods Phys. Res. A
Volume 635 Issue 1 Pages 92-102
Keywords Cosmic rays; Radio detection; Analysis software; Detector simulation
Abstract The advent of the Auger Engineering Radio Array (AERA) necessitates the development of a powerful framework for the analysis of radio measurements of cosmic ray air showers. As AERA performs “radio-hybrid” measurements of air shower radio emission in coincidence with the surface particle detectors and fluorescence telescopes of the Pierre Auger Observatory, the radio analysis functionality had to be incorporated in the existing hybrid analysis solutions for fluorescence and surface detector data. This goal has been achieved in a natural way by extending the existing Auger Offline software framework with radio functionality. In this article, we lay out the design, highlights and features of the radio extension implemented in the Auger Offline framework. Its functionality has achieved a high degree of sophistication and offers advanced features such as vectorial reconstruction of the electric field, advanced signal processing algorithms, a transparent and efficient handling of FFTs, a very detailed simulation of detector effects, and the read-in of multiple data formats including data from various radio simulation codes. The source code of this radio functionality can be made available to interested parties on request.
Address [Becker, K. H.; Bleve, C.; Kampert, K. H.; Krohm, N.; Kruppke-Hansen, D.; Kuempel, D.; Nierstenhoefer, N.; Oliva, P.; Rautenberg, J.; Szadkowski, Z.; Tascau, O.] Berg Univ Wuppertal, Wuppertal, Germany, Email: auger_pc@fnal.gov
Corporate Author Thesis
Publisher Elsevier Science Bv Place of Publication Editor
Language English Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (up) 0168-9002 ISBN Medium
Area Expedition Conference
Notes ISI:000289317100017 Approved no
Is ISI yes International Collaboration yes
Call Number IFIC @ pastor @ Serial 606
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Author Langer, C.; Algora, A.; Couture, A.; Csatlos, M.; Gulyas, J.; Heil, M.; Krasznahorkay, A.; O'Donnell, J.M.; Plag, R.; Reifarth, R.; Stuhl, L.; Sonnabend, K.; Tornyi, T.; Tovesson, F.
Title Simulations and developments of the Low Energy Neutron detector Array LENA Type Journal Article
Year 2011 Publication Nuclear Instruments & Methods in Physics Research A Abbreviated Journal Nucl. Instrum. Methods Phys. Res. A
Volume 659 Issue 1 Pages 411-418
Keywords Monte Carlo simulations; Charge-exchange reactions; Scintillation detectors; Neutron detector
Abstract Prototypes of the Low Energy Neutron detector Array (LENA) have been tested and compared with detailed GEANT simulations. LENA will consist of plastic scintillation bars with the dimensions 1000 x 45 x 10 mm(3). The tests have been performed with gamma-ray sources and neutrons originating from the neutron-induced fission of (235)U. The simulations agreed very well with the measured response and were therefore used to simulate the response to mono-energetic neutrons with different detection thresholds. LENA will be used to detect low-energy neutrons from (p,n)-type reactions with low momentum transfer foreseen at the R(3)B and EXL setups at FAIR, Darmstadt.
Address [Langer, C.; Heil, M.; Plag, R.; Reifarth, R.] GSI Helmholtzzentrum Schwerionenforsch GmbH, D-64291 Darmstadt, Germany, Email: c.langer@gsi.de
Corporate Author Thesis
Publisher Elsevier Science Bv Place of Publication Editor
Language English Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN (up) 0168-9002 ISBN Medium
Area Expedition Conference
Notes WOS:000297826100057 Approved no
Is ISI yes International Collaboration yes
Call Number IFIC @ pastor @ Serial 833
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