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J M Udias - One of the best experts on this subject based on the ideXlab platform.
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Evaluation of PenelopeT Simulations of Biograph PET/CT Scanners
IEEE Transactions on Nuclear Science, 2016Co-Authors: K. M. Abushab, S Espana, J L Herraiz, E Vicente, J J Vaquero, B. W. Jakoby, J. Cal-gonzález, J M UdiasAbstract:Monte Carlo (MC) simulations are widely used in positron emission tomography (PET) for optimizing detector design, acquisition protocols, and evaluating corrections and reconstruction methods. PenelopeT is a MC code based on Penelope, for PET simulations which considers detector geometry, acquisition electronics and materials, and source definitions. While PenelopeT has been successfully employed and validated with small animal PET scanners, it required a proper validation with clinical PET scanners including time-of-flight (TOF) information. For this purpose, we chose the family of Biograph PET/CT scanners: the Biograph True-Point (B-TP), Biograph True-Point with TrueV (B-TPTV) and the Biograph mCT. They have similar block detectors and electronics, but a different number of rings and configuration. Some effective parameters of the simulations, such as the dead-time and the size of the reflectors in the detectors, were adjusted to reproduce the sensitivity and noise equivalent count (NEC) rate of the B-TPTV scanner. These parameters were then used to make predictions of experimental results such as sensitivity, NEC rate, spatial resolution, and scatter fraction (SF), from all the Biograph scanners and some variations of them (energy windows and additional rings of detectors). Predictions agree with the measured values for the three scanners, within 7% (sensitivity and NEC rate) and 5% (SF). The resolution obtained for the B-TPTV is slightly better (10%) than the experimental values. In conclusion, we have shown that PenelopeT is suitable for simulating and investigating clinical systems with good accuracy and short computational time, though some effort tuning of a few parameters of the scanners modeled may be needed in case that the full details of the scanners studied are not available.
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PenelopeT simulations of the Biograph ToF clinical PET scanner
2011 IEEE Nuclear Science Symposium Conference Record, 2011Co-Authors: K. M. Abushab, S Espana, J L Herraiz, E Vicente, J J Vaquero, B. W. Jakoby, J M UdiasAbstract:Monte Carlo simulations are widely used in positron emission tomography (PET) for optimizing detector design, acquisition protocols, as well as for developing and assessing corrections and reconstruction methods. PenelopeT is a Monte Carlo code for PET simulations which considers detector geometry, acquisition electronics and materials, and source definitions. PenelopeT is based on Penelope, a Monte Carlo code for the simulation of the transport in matter of electrons, positrons and photons, with energies up to 1 GeV. In this work we use PenelopeT to simulate the Biograph TruePoint (B-TP), Biograph TruePoint with TrueV (B-TPTV) and Biograph mCT PET/CT scanners. These configurations consist of three (B-TP) and four (B-TPTV and mCT) rings of 48 detector blocks. Each block comprises a 13 × 13 matrix of 4 × 4 × 20 mm3 LSO crystals. Simulations were adjusted to reproduce some experimental results from the actual scanners and validated by comparing their predictions to further experimental results. Sensitivity, spatial resolution, noise equivalent count (NEC) rate and scatter fraction (SF) were estimated. The simulations were then employed to estimate the optimum values of system parameters, such as energy and time coincidence windows and to assess the effect of system modifications (such as number of rings) on performance.
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Penelopet a monte carlo pet simulation tool based on Penelope features and validation
Physics in Medicine and Biology, 2009Co-Authors: S Espana, J L Herraiz, E Vicente, J J Vaquero, Manuel Desco, J M UdiasAbstract:Monte Carlo simulations play an important role in positron emission tomography (PET) imaging, as an essential tool for the research and development of new scanners and for advanced image reconstruction. PenelopeT, a PET-dedicated Monte Carlo tool, is presented and validated in this work. PenelopeT is based on Penelope, a Monte Carlo code for the simulation of the transport in matter of electrons, positrons and photons, with energies from a few hundred eV to 1 GeV. Penelope is robust, fast and very accurate, but it may be unfriendly to people not acquainted with the FORTRAN programming language. PenelopeT is an easy-to-use application which allows comprehensive simulations of PET systems within Penelope. Complex and realistic simulations can be set by modifying a few simple input text files. Different levels of output data are available for analysis, from sinogram and lines-of-response (LORs) histogramming to fully detailed list mode. These data can be further exploited with the preferred programming language, including ROOT. PenelopeT simulates PET systems based on crystal array blocks coupled to photodetectors and allows the user to define radioactive sources, detectors, shielding and other parts of the scanner. The acquisition chain is simulated in high level detail; for instance, the electronic processing can include pile-up rejection mechanisms and time stamping of events, if desired. This paper describes PenelopeT and shows the results of extensive validations and comparisons of simulations against real measurements from commercial acquisition systems. PenelopeT is being extensively employed to improve the image quality of commercial PET systems and for the development of new ones.
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Validation of PenelopeT against two small animal PET scanners
2007 IEEE Nuclear Science Symposium Conference Record, 2007Co-Authors: S Espana, J L Herraiz, E Vicente, J J Vaquero, E. Herranz, M. Desco, J M UdiasAbstract:PenelopeT is a Monte Carlo application based on Penelope. We present here the new features and results of validation tests for the new version of PenelopeT that has been compared against data from real scanners. PenelopeT was built as a powerful tool for PET simulation, it is easy to use, fast and very accurate. Recently, many improvements have been made in the code with the incorporation of a very realistic signal processing chain and by adding the possibility of running simulations in parallel mode on cluster computers. A comparison between data obtained with two small-animal scanners and the results of PenelopeT simulations has been performed. The small-animal PET scanners were an eXplore Vista DR (GEHC) and a partial-ring, rotating rPET (SUINSA medical systems). Intrinsic resolution, scatter fractions, noise equivalent count rates and sensitivity measurements for the real acquisitions and simulations were compared. NEMA protocol was applied using mouse-size and rat-size cylinders, spheres and line sources as phantoms. Results show small differences (less than 10%) between real acquisitions and simulated data, proving that PenelopeT is an accurate tool for PET simulations.
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PenelopeT, a Monte Carlo PET simulation toolkit based on Penelope: Features and Validation
2006 IEEE Nuclear Science Symposium Conference Record, 2006Co-Authors: S Espana, J L Herraiz, E Vicente, J J Vaquero, Manuel Desco, J M UdiasAbstract:Penelope is a Monte Carlo code that simulates the transport in matter of electrons, positrons and photons with energies from a few hundred of eV to 1 GeV. It is robust, fast and very accurate, but it may be unfriendly for people not acquainted with the FORTRAN programming language. We have developed a tookit (`PenelopeT') to prepare simulations of PET and SPECT within Penelope. Sophisticated simulations can be setup by modifying just a few simple input files. The output data can be generated at different levels of detail and can be analyzed afterwards with the preferred programming language or tools. In this work, we present the features of PenelopeT as well as validations against other dedicated PET simulation programs and two real scanners.
E Vicente - One of the best experts on this subject based on the ideXlab platform.
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Evaluation of PenelopeT Simulations of Biograph PET/CT Scanners
IEEE Transactions on Nuclear Science, 2016Co-Authors: K. M. Abushab, S Espana, J L Herraiz, E Vicente, J J Vaquero, B. W. Jakoby, J. Cal-gonzález, J M UdiasAbstract:Monte Carlo (MC) simulations are widely used in positron emission tomography (PET) for optimizing detector design, acquisition protocols, and evaluating corrections and reconstruction methods. PenelopeT is a MC code based on Penelope, for PET simulations which considers detector geometry, acquisition electronics and materials, and source definitions. While PenelopeT has been successfully employed and validated with small animal PET scanners, it required a proper validation with clinical PET scanners including time-of-flight (TOF) information. For this purpose, we chose the family of Biograph PET/CT scanners: the Biograph True-Point (B-TP), Biograph True-Point with TrueV (B-TPTV) and the Biograph mCT. They have similar block detectors and electronics, but a different number of rings and configuration. Some effective parameters of the simulations, such as the dead-time and the size of the reflectors in the detectors, were adjusted to reproduce the sensitivity and noise equivalent count (NEC) rate of the B-TPTV scanner. These parameters were then used to make predictions of experimental results such as sensitivity, NEC rate, spatial resolution, and scatter fraction (SF), from all the Biograph scanners and some variations of them (energy windows and additional rings of detectors). Predictions agree with the measured values for the three scanners, within 7% (sensitivity and NEC rate) and 5% (SF). The resolution obtained for the B-TPTV is slightly better (10%) than the experimental values. In conclusion, we have shown that PenelopeT is suitable for simulating and investigating clinical systems with good accuracy and short computational time, though some effort tuning of a few parameters of the scanners modeled may be needed in case that the full details of the scanners studied are not available.
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PenelopeT simulations of the Biograph ToF clinical PET scanner
2011 IEEE Nuclear Science Symposium Conference Record, 2011Co-Authors: K. M. Abushab, S Espana, J L Herraiz, E Vicente, J J Vaquero, B. W. Jakoby, J M UdiasAbstract:Monte Carlo simulations are widely used in positron emission tomography (PET) for optimizing detector design, acquisition protocols, as well as for developing and assessing corrections and reconstruction methods. PenelopeT is a Monte Carlo code for PET simulations which considers detector geometry, acquisition electronics and materials, and source definitions. PenelopeT is based on Penelope, a Monte Carlo code for the simulation of the transport in matter of electrons, positrons and photons, with energies up to 1 GeV. In this work we use PenelopeT to simulate the Biograph TruePoint (B-TP), Biograph TruePoint with TrueV (B-TPTV) and Biograph mCT PET/CT scanners. These configurations consist of three (B-TP) and four (B-TPTV and mCT) rings of 48 detector blocks. Each block comprises a 13 × 13 matrix of 4 × 4 × 20 mm3 LSO crystals. Simulations were adjusted to reproduce some experimental results from the actual scanners and validated by comparing their predictions to further experimental results. Sensitivity, spatial resolution, noise equivalent count (NEC) rate and scatter fraction (SF) were estimated. The simulations were then employed to estimate the optimum values of system parameters, such as energy and time coincidence windows and to assess the effect of system modifications (such as number of rings) on performance.
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Penelopet a monte carlo pet simulation tool based on Penelope features and validation
Physics in Medicine and Biology, 2009Co-Authors: S Espana, J L Herraiz, E Vicente, J J Vaquero, Manuel Desco, J M UdiasAbstract:Monte Carlo simulations play an important role in positron emission tomography (PET) imaging, as an essential tool for the research and development of new scanners and for advanced image reconstruction. PenelopeT, a PET-dedicated Monte Carlo tool, is presented and validated in this work. PenelopeT is based on Penelope, a Monte Carlo code for the simulation of the transport in matter of electrons, positrons and photons, with energies from a few hundred eV to 1 GeV. Penelope is robust, fast and very accurate, but it may be unfriendly to people not acquainted with the FORTRAN programming language. PenelopeT is an easy-to-use application which allows comprehensive simulations of PET systems within Penelope. Complex and realistic simulations can be set by modifying a few simple input text files. Different levels of output data are available for analysis, from sinogram and lines-of-response (LORs) histogramming to fully detailed list mode. These data can be further exploited with the preferred programming language, including ROOT. PenelopeT simulates PET systems based on crystal array blocks coupled to photodetectors and allows the user to define radioactive sources, detectors, shielding and other parts of the scanner. The acquisition chain is simulated in high level detail; for instance, the electronic processing can include pile-up rejection mechanisms and time stamping of events, if desired. This paper describes PenelopeT and shows the results of extensive validations and comparisons of simulations against real measurements from commercial acquisition systems. PenelopeT is being extensively employed to improve the image quality of commercial PET systems and for the development of new ones.
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Validation of PenelopeT against two small animal PET scanners
2007 IEEE Nuclear Science Symposium Conference Record, 2007Co-Authors: S Espana, J L Herraiz, E Vicente, J J Vaquero, E. Herranz, M. Desco, J M UdiasAbstract:PenelopeT is a Monte Carlo application based on Penelope. We present here the new features and results of validation tests for the new version of PenelopeT that has been compared against data from real scanners. PenelopeT was built as a powerful tool for PET simulation, it is easy to use, fast and very accurate. Recently, many improvements have been made in the code with the incorporation of a very realistic signal processing chain and by adding the possibility of running simulations in parallel mode on cluster computers. A comparison between data obtained with two small-animal scanners and the results of PenelopeT simulations has been performed. The small-animal PET scanners were an eXplore Vista DR (GEHC) and a partial-ring, rotating rPET (SUINSA medical systems). Intrinsic resolution, scatter fractions, noise equivalent count rates and sensitivity measurements for the real acquisitions and simulations were compared. NEMA protocol was applied using mouse-size and rat-size cylinders, spheres and line sources as phantoms. Results show small differences (less than 10%) between real acquisitions and simulated data, proving that PenelopeT is an accurate tool for PET simulations.
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PenelopeT, a Monte Carlo PET simulation toolkit based on Penelope: Features and Validation
2006 IEEE Nuclear Science Symposium Conference Record, 2006Co-Authors: S Espana, J L Herraiz, E Vicente, J J Vaquero, Manuel Desco, J M UdiasAbstract:Penelope is a Monte Carlo code that simulates the transport in matter of electrons, positrons and photons with energies from a few hundred of eV to 1 GeV. It is robust, fast and very accurate, but it may be unfriendly for people not acquainted with the FORTRAN programming language. We have developed a tookit (`PenelopeT') to prepare simulations of PET and SPECT within Penelope. Sophisticated simulations can be setup by modifying just a few simple input files. The output data can be generated at different levels of detail and can be analyzed afterwards with the preferred programming language or tools. In this work, we present the features of PenelopeT as well as validations against other dedicated PET simulation programs and two real scanners.
Michael B Evgenev - One of the best experts on this subject based on the ideXlab platform.
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Penelope like elements a new class of retroelements distribution function and possible evolutionary significance
Cytogenetic and Genome Research, 2005Co-Authors: Michael B Evgenev, Irina R ArkhipovaAbstract:Here we describe a new class of retroelements termed PLE ( Penelope -like elements). The only transpositionally active representative of this lineage found so far has been isolated fr
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reverse transcriptase and endonuclease activities encoded by Penelope like retroelements
Proceedings of the National Academy of Sciences of the United States of America, 2004Co-Authors: Konstantin Pyatkov, Irina R Arkhipova, David J Finnegan, N V Malkova, Michael B EvgenevAbstract:Penelope-like elements are a class of retroelement that have now been identified in >50 species belonging to at least 10 animal phyla. The Penelope element isolated from Drosophila virilis is the only transpositionally active representative of this class isolated so far. The single ORF of Penelope and its relatives contains regions homologous to a reverse transcriptase of atypical structure and to the GIY-YIG, or Uri, an endonuclease (EN) domain not previously found in retroelements. We have expressed the single ORF of Penelope in a baculovirus expression system and have shown that it encodes a polyprotein with reverse transcriptase activity that requires divalent cations (Mn2+ and Mg2+). We have also expressed and purified the EN domain in Escherichia coli and have demonstrated that it has EN activity in vitro. Mutations in the conserved residues of the EN catalytic module abolish its nicking activity, whereas the DNA-binding properties of the mutant proteins remain unaffected. Only one strand of the target sequence is cleaved, and there is a certain degree of cleavage specificity. We propose that the Penelope EN cleaves the target DNA during transposition, generating a primer for reverse transcription. Our results show that an active Uri EN has been adopted by a retrotransposon.
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Penelope retroelements from drosophila virilis are active after transformation of drosophila melanogaster
Proceedings of the National Academy of Sciences of the United States of America, 2002Co-Authors: Konstantin Pyatkov, E S Zelentsova, David J Finnegan, N G Shostak, George T Lyozin, Michael I Melekhin, Margaret G Kidwell, Michael B EvgenevAbstract:The Penelope family of retroelements was first described in species of the Drosophila virilis group. Intact elements encode a reverse transcriptase and an endonuclease of the UvrC type, which may play a role in Penelope integration. Penelope is a key element in the induction of D. virilis hybrid dysgenesis, which involves the mobilization of several unrelated families of transposable elements. We here report the successful introduction of Penelope into the germ line of Drosophila melanogaster by P element-mediated transformation with three different constructs. Penelope is actively transcribed in the D. melanogaster genome only in lines transformed with a construct containing a full-length Penelope clone. The transcript is identical to that detected in D. virilis dysgenic hybrids. Most newly transposed Penelope elements have a very complex organization. Significant proliferation of Penelope copy number occurred in some lines during the 24-month period after transformation. The absence of copy number increase with two other constructs suggests that the 5′ and/or 3′ UTRs of Penelope are required for successful transposition in D. melanogaster. No insect retroelement has previously been reported to be actively transcribed and to increase in copy number after interspecific transformation.
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the structure and evolution of Penelope in the virilis species group of drosophila an ancient lineage of retroelements
Journal of Molecular Evolution, 2001Co-Authors: George T Lyozin, Margaret G Kidwell, Kira S Makarova, Vera V Velikodvorskaja, Helena Zelentsova, Ruben R Khechumian, Eugene V Koonin, Michael B EvgenevAbstract:The Penelope element is the key element responsible for mobilization of other transposable elements in the course of hybrid dysgenesis in Drosophila virilis. Penelope has an unusually complex, highly variable organization in all studied species of the virlis group. Thc BRIDGE1 element from the fish Fugu rubripes is homologous to Penelope, and database searches detected additional homologous sequences among Expressed Sequence Tags from the flatworm Schistosoma mansonii and the nematode Ancylostoma caninum. Phylogenetic analysis shows that the reverse transcriptase of the Penelope group does not belong to any of the characterized major retroelement lineages, but apparently represents a novel branch of non-LTR retroelements. Sequence profile analysis results in the prediction that the C-terminal domain of the Penelope polyprotein is an active endonuclease related to intron-encoded endonucleases and the bacterial repair endonuclease UvrC, which could function as an integrase. No retroelements containing a predicted endonuclease of this family have been described previously. Phylogenetic analysis of Penelope copies isolated from several species of the virilis group reveals two subfamilies of Penelope elements, one of which includes full-length copies whose nucleotide sequences are almost identical, whereas the other one consists of highly diverged defective copies. Phylogenetic analysis of Penelope suggests both vertical transmission of the element and probable horizontal transfers. These findings support the notion that Penelope invasions occurred repeatedly in the evolution of the virilis group.
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Penelope a new family of transposable elements and its possible role in hybrid dysgenesis in drosophila virilis
Proceedings of the National Academy of Sciences of the United States of America, 1997Co-Authors: Michael B Evgenev, N G Shostak, Helena Zelentsova, Marina Kozitsina, Victor Barskyi, Dirkhenner Lankenau, Victor G CorcesAbstract:A hybrid dysgenesis syndrome occurs in Drosophila virilis when males from an established laboratory strain are crossed to females obtained from the wild, causing the simultaneous mobilization of several different transposable elements. The insertion sequence responsible for the mutant phenotype of a dysgenic yellow allele has been characterized and named Penelope. In situ hybridization and Southern analyses reveal the presence of more than 30 copies of this element in the P-like parental strain, whereas Penelope is absent in all M-like strains tested. Penelope contains one 2.5-kb-long ORF that could encode products with homology to integrase and reverse transcriptase. Northern analysis and whole-mount in situ hybridization show strong induction of a 2.6-kb RNA in the ovaries of dysgenic females that is expressed at very low levels in the parental strains or in the progeny from the reciprocal cross. Injection of Penelope-containing plasmids into preblastoderm embryos of an M-like strain results in mutant progeny caused by insertion of Ulysses and perhaps other transposons, suggesting that Penelope expression might be responsible for the observed dysgenesis syndrome and the simultaneous mobilization of other transposable elements.
S Espana - One of the best experts on this subject based on the ideXlab platform.
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Evaluation of PenelopeT Simulations of Biograph PET/CT Scanners
IEEE Transactions on Nuclear Science, 2016Co-Authors: K. M. Abushab, S Espana, J L Herraiz, E Vicente, J J Vaquero, B. W. Jakoby, J. Cal-gonzález, J M UdiasAbstract:Monte Carlo (MC) simulations are widely used in positron emission tomography (PET) for optimizing detector design, acquisition protocols, and evaluating corrections and reconstruction methods. PenelopeT is a MC code based on Penelope, for PET simulations which considers detector geometry, acquisition electronics and materials, and source definitions. While PenelopeT has been successfully employed and validated with small animal PET scanners, it required a proper validation with clinical PET scanners including time-of-flight (TOF) information. For this purpose, we chose the family of Biograph PET/CT scanners: the Biograph True-Point (B-TP), Biograph True-Point with TrueV (B-TPTV) and the Biograph mCT. They have similar block detectors and electronics, but a different number of rings and configuration. Some effective parameters of the simulations, such as the dead-time and the size of the reflectors in the detectors, were adjusted to reproduce the sensitivity and noise equivalent count (NEC) rate of the B-TPTV scanner. These parameters were then used to make predictions of experimental results such as sensitivity, NEC rate, spatial resolution, and scatter fraction (SF), from all the Biograph scanners and some variations of them (energy windows and additional rings of detectors). Predictions agree with the measured values for the three scanners, within 7% (sensitivity and NEC rate) and 5% (SF). The resolution obtained for the B-TPTV is slightly better (10%) than the experimental values. In conclusion, we have shown that PenelopeT is suitable for simulating and investigating clinical systems with good accuracy and short computational time, though some effort tuning of a few parameters of the scanners modeled may be needed in case that the full details of the scanners studied are not available.
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PenelopeT simulations of the Biograph ToF clinical PET scanner
2011 IEEE Nuclear Science Symposium Conference Record, 2011Co-Authors: K. M. Abushab, S Espana, J L Herraiz, E Vicente, J J Vaquero, B. W. Jakoby, J M UdiasAbstract:Monte Carlo simulations are widely used in positron emission tomography (PET) for optimizing detector design, acquisition protocols, as well as for developing and assessing corrections and reconstruction methods. PenelopeT is a Monte Carlo code for PET simulations which considers detector geometry, acquisition electronics and materials, and source definitions. PenelopeT is based on Penelope, a Monte Carlo code for the simulation of the transport in matter of electrons, positrons and photons, with energies up to 1 GeV. In this work we use PenelopeT to simulate the Biograph TruePoint (B-TP), Biograph TruePoint with TrueV (B-TPTV) and Biograph mCT PET/CT scanners. These configurations consist of three (B-TP) and four (B-TPTV and mCT) rings of 48 detector blocks. Each block comprises a 13 × 13 matrix of 4 × 4 × 20 mm3 LSO crystals. Simulations were adjusted to reproduce some experimental results from the actual scanners and validated by comparing their predictions to further experimental results. Sensitivity, spatial resolution, noise equivalent count (NEC) rate and scatter fraction (SF) were estimated. The simulations were then employed to estimate the optimum values of system parameters, such as energy and time coincidence windows and to assess the effect of system modifications (such as number of rings) on performance.
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Penelopet a monte carlo pet simulation tool based on Penelope features and validation
Physics in Medicine and Biology, 2009Co-Authors: S Espana, J L Herraiz, E Vicente, J J Vaquero, Manuel Desco, J M UdiasAbstract:Monte Carlo simulations play an important role in positron emission tomography (PET) imaging, as an essential tool for the research and development of new scanners and for advanced image reconstruction. PenelopeT, a PET-dedicated Monte Carlo tool, is presented and validated in this work. PenelopeT is based on Penelope, a Monte Carlo code for the simulation of the transport in matter of electrons, positrons and photons, with energies from a few hundred eV to 1 GeV. Penelope is robust, fast and very accurate, but it may be unfriendly to people not acquainted with the FORTRAN programming language. PenelopeT is an easy-to-use application which allows comprehensive simulations of PET systems within Penelope. Complex and realistic simulations can be set by modifying a few simple input text files. Different levels of output data are available for analysis, from sinogram and lines-of-response (LORs) histogramming to fully detailed list mode. These data can be further exploited with the preferred programming language, including ROOT. PenelopeT simulates PET systems based on crystal array blocks coupled to photodetectors and allows the user to define radioactive sources, detectors, shielding and other parts of the scanner. The acquisition chain is simulated in high level detail; for instance, the electronic processing can include pile-up rejection mechanisms and time stamping of events, if desired. This paper describes PenelopeT and shows the results of extensive validations and comparisons of simulations against real measurements from commercial acquisition systems. PenelopeT is being extensively employed to improve the image quality of commercial PET systems and for the development of new ones.
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Validation of PenelopeT against two small animal PET scanners
2007 IEEE Nuclear Science Symposium Conference Record, 2007Co-Authors: S Espana, J L Herraiz, E Vicente, J J Vaquero, E. Herranz, M. Desco, J M UdiasAbstract:PenelopeT is a Monte Carlo application based on Penelope. We present here the new features and results of validation tests for the new version of PenelopeT that has been compared against data from real scanners. PenelopeT was built as a powerful tool for PET simulation, it is easy to use, fast and very accurate. Recently, many improvements have been made in the code with the incorporation of a very realistic signal processing chain and by adding the possibility of running simulations in parallel mode on cluster computers. A comparison between data obtained with two small-animal scanners and the results of PenelopeT simulations has been performed. The small-animal PET scanners were an eXplore Vista DR (GEHC) and a partial-ring, rotating rPET (SUINSA medical systems). Intrinsic resolution, scatter fractions, noise equivalent count rates and sensitivity measurements for the real acquisitions and simulations were compared. NEMA protocol was applied using mouse-size and rat-size cylinders, spheres and line sources as phantoms. Results show small differences (less than 10%) between real acquisitions and simulated data, proving that PenelopeT is an accurate tool for PET simulations.
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PenelopeT, a Monte Carlo PET simulation toolkit based on Penelope: Features and Validation
2006 IEEE Nuclear Science Symposium Conference Record, 2006Co-Authors: S Espana, J L Herraiz, E Vicente, J J Vaquero, Manuel Desco, J M UdiasAbstract:Penelope is a Monte Carlo code that simulates the transport in matter of electrons, positrons and photons with energies from a few hundred of eV to 1 GeV. It is robust, fast and very accurate, but it may be unfriendly for people not acquainted with the FORTRAN programming language. We have developed a tookit (`PenelopeT') to prepare simulations of PET and SPECT within Penelope. Sophisticated simulations can be setup by modifying just a few simple input files. The output data can be generated at different levels of detail and can be analyzed afterwards with the preferred programming language or tools. In this work, we present the features of PenelopeT as well as validations against other dedicated PET simulation programs and two real scanners.
J L Herraiz - One of the best experts on this subject based on the ideXlab platform.
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Evaluation of PenelopeT Simulations of Biograph PET/CT Scanners
IEEE Transactions on Nuclear Science, 2016Co-Authors: K. M. Abushab, S Espana, J L Herraiz, E Vicente, J J Vaquero, B. W. Jakoby, J. Cal-gonzález, J M UdiasAbstract:Monte Carlo (MC) simulations are widely used in positron emission tomography (PET) for optimizing detector design, acquisition protocols, and evaluating corrections and reconstruction methods. PenelopeT is a MC code based on Penelope, for PET simulations which considers detector geometry, acquisition electronics and materials, and source definitions. While PenelopeT has been successfully employed and validated with small animal PET scanners, it required a proper validation with clinical PET scanners including time-of-flight (TOF) information. For this purpose, we chose the family of Biograph PET/CT scanners: the Biograph True-Point (B-TP), Biograph True-Point with TrueV (B-TPTV) and the Biograph mCT. They have similar block detectors and electronics, but a different number of rings and configuration. Some effective parameters of the simulations, such as the dead-time and the size of the reflectors in the detectors, were adjusted to reproduce the sensitivity and noise equivalent count (NEC) rate of the B-TPTV scanner. These parameters were then used to make predictions of experimental results such as sensitivity, NEC rate, spatial resolution, and scatter fraction (SF), from all the Biograph scanners and some variations of them (energy windows and additional rings of detectors). Predictions agree with the measured values for the three scanners, within 7% (sensitivity and NEC rate) and 5% (SF). The resolution obtained for the B-TPTV is slightly better (10%) than the experimental values. In conclusion, we have shown that PenelopeT is suitable for simulating and investigating clinical systems with good accuracy and short computational time, though some effort tuning of a few parameters of the scanners modeled may be needed in case that the full details of the scanners studied are not available.
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PenelopeT simulations of the Biograph ToF clinical PET scanner
2011 IEEE Nuclear Science Symposium Conference Record, 2011Co-Authors: K. M. Abushab, S Espana, J L Herraiz, E Vicente, J J Vaquero, B. W. Jakoby, J M UdiasAbstract:Monte Carlo simulations are widely used in positron emission tomography (PET) for optimizing detector design, acquisition protocols, as well as for developing and assessing corrections and reconstruction methods. PenelopeT is a Monte Carlo code for PET simulations which considers detector geometry, acquisition electronics and materials, and source definitions. PenelopeT is based on Penelope, a Monte Carlo code for the simulation of the transport in matter of electrons, positrons and photons, with energies up to 1 GeV. In this work we use PenelopeT to simulate the Biograph TruePoint (B-TP), Biograph TruePoint with TrueV (B-TPTV) and Biograph mCT PET/CT scanners. These configurations consist of three (B-TP) and four (B-TPTV and mCT) rings of 48 detector blocks. Each block comprises a 13 × 13 matrix of 4 × 4 × 20 mm3 LSO crystals. Simulations were adjusted to reproduce some experimental results from the actual scanners and validated by comparing their predictions to further experimental results. Sensitivity, spatial resolution, noise equivalent count (NEC) rate and scatter fraction (SF) were estimated. The simulations were then employed to estimate the optimum values of system parameters, such as energy and time coincidence windows and to assess the effect of system modifications (such as number of rings) on performance.
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Penelopet a monte carlo pet simulation tool based on Penelope features and validation
Physics in Medicine and Biology, 2009Co-Authors: S Espana, J L Herraiz, E Vicente, J J Vaquero, Manuel Desco, J M UdiasAbstract:Monte Carlo simulations play an important role in positron emission tomography (PET) imaging, as an essential tool for the research and development of new scanners and for advanced image reconstruction. PenelopeT, a PET-dedicated Monte Carlo tool, is presented and validated in this work. PenelopeT is based on Penelope, a Monte Carlo code for the simulation of the transport in matter of electrons, positrons and photons, with energies from a few hundred eV to 1 GeV. Penelope is robust, fast and very accurate, but it may be unfriendly to people not acquainted with the FORTRAN programming language. PenelopeT is an easy-to-use application which allows comprehensive simulations of PET systems within Penelope. Complex and realistic simulations can be set by modifying a few simple input text files. Different levels of output data are available for analysis, from sinogram and lines-of-response (LORs) histogramming to fully detailed list mode. These data can be further exploited with the preferred programming language, including ROOT. PenelopeT simulates PET systems based on crystal array blocks coupled to photodetectors and allows the user to define radioactive sources, detectors, shielding and other parts of the scanner. The acquisition chain is simulated in high level detail; for instance, the electronic processing can include pile-up rejection mechanisms and time stamping of events, if desired. This paper describes PenelopeT and shows the results of extensive validations and comparisons of simulations against real measurements from commercial acquisition systems. PenelopeT is being extensively employed to improve the image quality of commercial PET systems and for the development of new ones.
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Validation of PenelopeT against two small animal PET scanners
2007 IEEE Nuclear Science Symposium Conference Record, 2007Co-Authors: S Espana, J L Herraiz, E Vicente, J J Vaquero, E. Herranz, M. Desco, J M UdiasAbstract:PenelopeT is a Monte Carlo application based on Penelope. We present here the new features and results of validation tests for the new version of PenelopeT that has been compared against data from real scanners. PenelopeT was built as a powerful tool for PET simulation, it is easy to use, fast and very accurate. Recently, many improvements have been made in the code with the incorporation of a very realistic signal processing chain and by adding the possibility of running simulations in parallel mode on cluster computers. A comparison between data obtained with two small-animal scanners and the results of PenelopeT simulations has been performed. The small-animal PET scanners were an eXplore Vista DR (GEHC) and a partial-ring, rotating rPET (SUINSA medical systems). Intrinsic resolution, scatter fractions, noise equivalent count rates and sensitivity measurements for the real acquisitions and simulations were compared. NEMA protocol was applied using mouse-size and rat-size cylinders, spheres and line sources as phantoms. Results show small differences (less than 10%) between real acquisitions and simulated data, proving that PenelopeT is an accurate tool for PET simulations.
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PenelopeT, a Monte Carlo PET simulation toolkit based on Penelope: Features and Validation
2006 IEEE Nuclear Science Symposium Conference Record, 2006Co-Authors: S Espana, J L Herraiz, E Vicente, J J Vaquero, Manuel Desco, J M UdiasAbstract:Penelope is a Monte Carlo code that simulates the transport in matter of electrons, positrons and photons with energies from a few hundred of eV to 1 GeV. It is robust, fast and very accurate, but it may be unfriendly for people not acquainted with the FORTRAN programming language. We have developed a tookit (`PenelopeT') to prepare simulations of PET and SPECT within Penelope. Sophisticated simulations can be setup by modifying just a few simple input files. The output data can be generated at different levels of detail and can be analyzed afterwards with the preferred programming language or tools. In this work, we present the features of PenelopeT as well as validations against other dedicated PET simulation programs and two real scanners.
