The Experts below are selected from a list of 180 Experts worldwide ranked by ideXlab platform
C M - One of the best experts on this subject based on the ideXlab platform.
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Particle Selection for laser accelerated proton therapy feasibility study
Medical Physics, 2003Co-Authors: E Fourkal, M Ding, T Tajima, C MAbstract:In this paper we present calculations for the design of a Particle Selection system for laser-accelerated proton therapy. Laser-accelerated protons coming from a thin high-density foil have broad energy and angular spectra leading to dose distributions that cannot be directly used for therapeutic applications. Our solution to this problem is a compact Particle Selection and collimation device that delivers small pencil beams of protons with desired energy spectra. We propose a spectrometer-like Particle Selection and beam modulation system in which the magnetic field will be used to spread the protonsspatially according to their energies and emitting angles. Subsequently, an aperture will be used to select the protons within a therapeutic window of energy (energy modulation). It will be shown that for the effective proton spatial differentiation, the primary collimation device should be used, which will collimate protons to the desired angular distribution and limit the spatial mixing of different energy protons once they have traveled through the magnetic system. Due to the angular proton distribution, the spatial mixing of protons of different energies will always be present and it will result in a proton energy spread with the width depending on the energy. For 250 MeV protons, the width (from the maximum to the minimum energy) is found to be 50 MeV for the magnetic field configuration used in our calculations. As the proton energy decreases, its energy width decreases as well, and for 80 MeV protons it equals 9 MeV. The presence of the energy width in the proton energy distribution will modify the depth dose curves needed for the energy modulation calculation. The matching magnetic field setup will ensure the refocusing of the selected protons and the final beam will be collimated by the secondary collimator. The calculations presented in this article show that the dose rate that the Selection system can yield is on the order of D=260 Gy/min for a field size of 1×1 cm2.
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Particle in cell simulation of laser accelerated proton beams for radiation therapy
Medical Physics, 2002Co-Authors: E Fourkal, M Ding, T Tajima, C M, B ShahineAbstract:In this article we present the results of Particle in cell (PIC) simulations of laser plasma interaction for proton acceleration for radiation therapy treatments. We show that under optimal interaction conditions protons can be accelerated up to relativistic energies of 300 MeV by a petawatt laser field. The proton acceleration is due to the dragging Coulomb force arising from charge separation induced by the ponderomotive pressure (light pressure) of high-intensity laser. The proton energy and phase space distribution functions obtained from the PIC simulations are used in the calculations of dose distributions using the GEANT Monte Carlo simulation code. Because of the broad energy and angular spectra of the protons, a compact Particle Selection and beam collimation system will be needed to generate small beams of polyenergetic protons for intensity modulated proton therapy.
E Fourkal - One of the best experts on this subject based on the ideXlab platform.
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Particle Selection for laser accelerated proton therapy feasibility study
Medical Physics, 2003Co-Authors: E Fourkal, M Ding, T Tajima, C MAbstract:In this paper we present calculations for the design of a Particle Selection system for laser-accelerated proton therapy. Laser-accelerated protons coming from a thin high-density foil have broad energy and angular spectra leading to dose distributions that cannot be directly used for therapeutic applications. Our solution to this problem is a compact Particle Selection and collimation device that delivers small pencil beams of protons with desired energy spectra. We propose a spectrometer-like Particle Selection and beam modulation system in which the magnetic field will be used to spread the protonsspatially according to their energies and emitting angles. Subsequently, an aperture will be used to select the protons within a therapeutic window of energy (energy modulation). It will be shown that for the effective proton spatial differentiation, the primary collimation device should be used, which will collimate protons to the desired angular distribution and limit the spatial mixing of different energy protons once they have traveled through the magnetic system. Due to the angular proton distribution, the spatial mixing of protons of different energies will always be present and it will result in a proton energy spread with the width depending on the energy. For 250 MeV protons, the width (from the maximum to the minimum energy) is found to be 50 MeV for the magnetic field configuration used in our calculations. As the proton energy decreases, its energy width decreases as well, and for 80 MeV protons it equals 9 MeV. The presence of the energy width in the proton energy distribution will modify the depth dose curves needed for the energy modulation calculation. The matching magnetic field setup will ensure the refocusing of the selected protons and the final beam will be collimated by the secondary collimator. The calculations presented in this article show that the dose rate that the Selection system can yield is on the order of D=260 Gy/min for a field size of 1×1 cm2.
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Particle in cell simulation of laser accelerated proton beams for radiation therapy
Medical Physics, 2002Co-Authors: E Fourkal, M Ding, T Tajima, C M, B ShahineAbstract:In this article we present the results of Particle in cell (PIC) simulations of laser plasma interaction for proton acceleration for radiation therapy treatments. We show that under optimal interaction conditions protons can be accelerated up to relativistic energies of 300 MeV by a petawatt laser field. The proton acceleration is due to the dragging Coulomb force arising from charge separation induced by the ponderomotive pressure (light pressure) of high-intensity laser. The proton energy and phase space distribution functions obtained from the PIC simulations are used in the calculations of dose distributions using the GEANT Monte Carlo simulation code. Because of the broad energy and angular spectra of the protons, a compact Particle Selection and beam collimation system will be needed to generate small beams of polyenergetic protons for intensity modulated proton therapy.
Joachim Frank - One of the best experts on this subject based on the ideXlab platform.
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reference free Particle Selection enhanced with semi supervised machine learning for cryo electron microscopy
Journal of Structural Biology, 2011Co-Authors: Robert Langlois, Jesper Pallesen, Joachim FrankAbstract:Abstract Reference-based methods have dominated the approaches to the Particle Selection problem, proving fast, and accurate on even the most challenging micrographs. A reference volume, however, is not always available and compiling a set of reference projections from the micrographs themselves requires significant effort to attain the same level of accuracy. We propose a reference-free method to quickly extract Particles from the micrograph. The method is augmented with a new semi-supervised machine-learning algorithm to accurately discriminate Particles from contaminants and noise.
M Ding - One of the best experts on this subject based on the ideXlab platform.
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Particle Selection for laser accelerated proton therapy feasibility study
Medical Physics, 2003Co-Authors: E Fourkal, M Ding, T Tajima, C MAbstract:In this paper we present calculations for the design of a Particle Selection system for laser-accelerated proton therapy. Laser-accelerated protons coming from a thin high-density foil have broad energy and angular spectra leading to dose distributions that cannot be directly used for therapeutic applications. Our solution to this problem is a compact Particle Selection and collimation device that delivers small pencil beams of protons with desired energy spectra. We propose a spectrometer-like Particle Selection and beam modulation system in which the magnetic field will be used to spread the protonsspatially according to their energies and emitting angles. Subsequently, an aperture will be used to select the protons within a therapeutic window of energy (energy modulation). It will be shown that for the effective proton spatial differentiation, the primary collimation device should be used, which will collimate protons to the desired angular distribution and limit the spatial mixing of different energy protons once they have traveled through the magnetic system. Due to the angular proton distribution, the spatial mixing of protons of different energies will always be present and it will result in a proton energy spread with the width depending on the energy. For 250 MeV protons, the width (from the maximum to the minimum energy) is found to be 50 MeV for the magnetic field configuration used in our calculations. As the proton energy decreases, its energy width decreases as well, and for 80 MeV protons it equals 9 MeV. The presence of the energy width in the proton energy distribution will modify the depth dose curves needed for the energy modulation calculation. The matching magnetic field setup will ensure the refocusing of the selected protons and the final beam will be collimated by the secondary collimator. The calculations presented in this article show that the dose rate that the Selection system can yield is on the order of D=260 Gy/min for a field size of 1×1 cm2.
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Particle in cell simulation of laser accelerated proton beams for radiation therapy
Medical Physics, 2002Co-Authors: E Fourkal, M Ding, T Tajima, C M, B ShahineAbstract:In this article we present the results of Particle in cell (PIC) simulations of laser plasma interaction for proton acceleration for radiation therapy treatments. We show that under optimal interaction conditions protons can be accelerated up to relativistic energies of 300 MeV by a petawatt laser field. The proton acceleration is due to the dragging Coulomb force arising from charge separation induced by the ponderomotive pressure (light pressure) of high-intensity laser. The proton energy and phase space distribution functions obtained from the PIC simulations are used in the calculations of dose distributions using the GEANT Monte Carlo simulation code. Because of the broad energy and angular spectra of the protons, a compact Particle Selection and beam collimation system will be needed to generate small beams of polyenergetic protons for intensity modulated proton therapy.
Bridget Carragher - One of the best experts on this subject based on the ideXlab platform.
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dog picker and tiltpicker software tools to facilitate Particle Selection in single Particle electron microscopy
Journal of Structural Biology, 2009Co-Authors: Neil R Voss, Clinton S Potter, Craig Yoshioka, Michael Radermacher, Bridget CarragherAbstract:Solving the structure of macromolecular complexes using transmission electron microscopy can be an arduous task. Many of the steps in this process rely strongly on the aid of pre-existing structural knowledge, and are greatly complicated when this information is unavailable. Here, we present two software tools meant to facilitate Particle picking, an early stage in the single-Particle processing of unknown macromolecules. The first tool, DoG Picker, is an efficient and reasonably general, Particle picker based on the Difference of Gaussians (DoG) image transform. It can function alone, as a reference-free Particle picker with the unique ability to sort Particles based on size, or it can also be used as a way to bootstrap the creation of templates or training datasets for other Particle pickers. The second tool is TiltPicker, an interactive graphical interface application designed to streamline the Selection of Particle pairs from tilted-pair datasets. In many respects, TiltPicker is a re-implementation of the SPIDER WEB tilted-Particle picker, but built on modern computer frameworks making it easier to deploy and maintain. The TiltPicker program also includes several useful new features beyond those of its predecessor.
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automatic Particle Selection results of a comparative study
Journal of Structural Biology, 2004Co-Authors: Yuanxin Zhu, Fabrice Mouche, Bridget Carragher, Robert M Glaeser, Denis Fellmann, Chandrajit L Bajaj, Marshall Bern, Felix De Haas, Richard Hall, David J KriegmanAbstract:Manual Selection of single Particles in images acquired using cryo-electron microscopy (cryoEM) will become a significant bottleneck when datasets of a hundred thousand or even a million Particles are required for structure determination at near atomic resolution. Algorithm development of fully automated Particle Selection is thus an important research objective in the cryoEM field. A number of research groups are making promising new advances in this area. Evaluation of algorithms using a standard set of cryoEM images is an essential aspect of this algorithm development. With this goal in mind, a Particle Selection "bakeoff" was included in the program of the Multidisciplinary Workshop on Automatic Particle Selection for cryoEM. Twelve groups participated by submitting the results of testing their own algorithms on a common dataset. The dataset consisted of 82 defocus pairs of high-magnification micrographs, containing keyhole limpet hemocyanin Particles, acquired using cryoEM. The results of the bakeoff are presented in this paper along with a summary of the discussion from the workshop. It was agreed that establishing benchmark Particles and using bakeoffs to evaluate algorithms are useful in promoting algorithm development for fully automated Particle Selection, and that the infrastructure set up to support the bakeoff should be maintained and extended to include larger and more varied datasets, and more criteria for future evaluations.
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automated three dimensional reconstruction of keyhole limpet hemocyanin type 1
Journal of Structural Biology, 2003Co-Authors: Fabrice Mouche, Yuanxin Zhu, James Pulokas, Clinton S Potter, Bridget CarragherAbstract:Abstract We have reconstructed a three-dimensional map of keyhole limpet hemocyanin isoform 1 (KLH1), using our automated data collection software, Leginon, integrated with Particle Selection algorithms, and the SPIDER reconstruction package. KLH1, a 7.9 MDa macromolecule, is an extracellular respiratory pigment composed of two asymmetric decamers, and presents an overall D 5 point-group symmetry. The reconstruction is in agreement with previous data published on molluscan hemocyanins. The reconstructed map (11.3 A resolution, 3 σ criterion) was used to fit an available X-ray crystallography structure of Octopus dofleini Odg , solved at 2.3 A [J. Mol. Biol. 278 (4) (1998) 855], with satisfactory results. The results validate the approach of automating the cryoEM process and demonstrate that the quality of the images acquired and the Particles selected is comparable to those obtained using manual methods. Several problems remain to be solved however before these results can be generalized.