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'''Wiki for the proton CT project'''
'''Wiki for the proton CT project'''


== [[Documentation]] ==
== Documentation and Howto's ==
[[Documentation]] on how to install and use the involved software packages, the development workflow, etc.
=== Software ===
* [[Documentation|Software Documentation]] on how to install and use the involved software packages, how to use the GitLab service, and about the development workflow, etc.
 
=== Hardware ===
* [[Hardware Documentation and Howto's]] on pReadout, ALPIDE bonding, Production Test Box, Transition Card
 
=== Control & Readout Software ===
* [[Control & Readout Software Documentation and Howto's]]
 
=== ALPIDE ===
* [[ALPIDE Documentation and Papers]]
 
=== Cooling ===
[[Cooling Documentation]] on the cooling simulations, measurements, laboratory setup and the final design.
 
=== Århus Testbeam 2023 ===
[[Århus Testbeam 2023 Documentation]] on the testbeam at Århus hospital including simulation, setup, equipment used, etc.  


== [[Publications]] ==
== [[Publications]] ==
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* [http://bora.uib.no/handle/1956/18058 Viljar Nilsen Ekeland - MSc - 2018 - Characterization of the ALPIDE chip using protons (Data from Oslo beam test, cluster size and LET correlation with different bias voltages).]
* [http://bora.uib.no/handle/1956/18058 Viljar Nilsen Ekeland - MSc - 2018 - Characterization of the ALPIDE chip using protons (Data from Oslo beam test, cluster size and LET correlation with different bias voltages).]
* [http://bora.uib.no/handle/1956/18057 Susmita Afroz - MSc - 2018 - Noise and Cluster Size Studies of ALPIDE-CMOS Pixel Sensor for pCT]
* [http://bora.uib.no/handle/1956/18057 Susmita Afroz - MSc - 2018 - Noise and Cluster Size Studies of ALPIDE-CMOS Pixel Sensor for pCT]
* Silje Grimstad - MSc (HVL) - 2019 - ALPIDE Cluster simulations (Building database of cluster characteristics, simulation of clusters using said database. Position and cluster separation algorithms).
* [http://bora.uib.no/handle/1956/20846/ Håkon Andreas Underdal - MSc (HVL) - 2019 - Data Acquisition and Testing Software for a Proton Computed Tomography System  ]
* Alba Garcia Santos - MSc (Utrecht) - 2019 - Improvements of track reconstruction algorithms in pixel-based pCT calorimeters
* [http://bora.uib.no/handle/1956/20857  Silje Grimstad - MSc (HVL) - 2019 - ALPIDE Cluster simulations (Building database of cluster characteristics, simulation of clusters using said database. Position and cluster separation algorithms)].
* Aleksei Kuleshov - MSc - 2019 - Proton CT monitoring and ALPIDE control (MQTT protocol server, System workflow, GUI implementation).
* [http://resolver.tudelft.nl/uuid:e8d3f687-43ff-4d5f-a594-2e7d805f146b Alba Garcia Santos - MSc (Utrecht) - 2019 - Improvements of track reconstruction algorithms in pixel-based pCT calorimeters]
* [https://hdl.handle.net/1956/21101 Aleksei Kuleshov - MSc - 2019 - Proton CT monitoring and ALPIDE control (MQTT protocol server, System workflow, GUI implementation).]
* [https://bora.uib.no/bora-xmlui/handle/1956/24109 Øistein Jelmert Skjolddal - MSc (HVL) - 2020 Scalable Readout for Proton CT - pRU parser and Root interface.]
* [https://bora.uib.no/bora-xmlui/handle/11250/2716854 Jarle Rambo Sølie - PhD (HVL/UiB) - 2020 A Monte Carlo simulation framework for performance evaluation of a proton imaging system without front trackers.]
* [https://hdl.handle.net/11250/2725567 Ola Grøttvik - PhD (UiB) - 2021 Design and Implementation of a High-Speed Readout and Control System for a Digital Tracking Calorimeter for proton CT.]
* [https://hdl.handle.net/11250/2770399 Alf Kristoffer Herland - MSc (HVL) - 2021 Development and implementation of data acquisition software for proton computed tomography.]
* [https://bora.uib.no/bora-xmlui/handle/11250/3013935 Rune Almåsbakk - MSc (HVL) - 2022 Design and Implementation of Alignment software for a Digital Tracking Calorimeter used for proton CT.]
* [https://bora.uib.no/bora-xmlui/handle/11250/3045481 Håvard Birkenes - MSc (UiB) - Design of a Configuration and Monitoring System for the Power Supply in the ProtonCT Project.]
* [https://bora.uib.no/bora-xmlui/handle/11250/3076410 Alfred Abbasi - MSc (UiB) - 2023 Hardware and Software Studies for the Alignment of the Proton CT.]
* [https://bora.uib.no/bora-xmlui/handle/11250/3072130 Jakub Bieniek - MSc (UiB) - 2023 Commisioning of the Cooling System for the Bergen Proton Computed Tomography Digital Tracking Calorimeter.]


==== Journal Articles ====
==== Journal Articles ====
* Aehle, M.,  et al. <b>Exploration of differentiability in a proton computed tomography simulation framework</b> <i> Physics in Medicine and Biology</i>  2023;68(244002).
** UiB archive: [ http://hdl.handle.net/10852/106386 ]
** IOP Science link: [https://iopscience.iop.org/article/10.1088/1361-6560/ad0bdd doi:10.1088/1361-6560/ad0bdd]
* Schilling, A.,  et al. <b>Towards Neural Charged Particle Tracking in Digital Tracking Calorimeters With Reinforcement Learning</b> <i>Physics in Medicine and Biology</i>  2023;68(194001).
** UiB archive: [ https://hdl.handle.net/11250/3100524 ]
** IOP Science link: [https://iopscience.iop.org/article/10.1088/1361-6560/acf5c2 doi:10.1109/TPAMI.2023.3305027]</b>
* Kortus, T.,  et al. <b>Towards Neural Charged Particle Tracking in Digital Tracking Calorimeters With Reinforcement Learning</b> <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>  2023;45(15820).
** UiB archive: [ http://hdl.handle.net/10852/106386 ]
** IEEE link: [https://ieeexplore.ieee.org/document/10219056 doi:10.1088/1361-6560/acf5c2]
* Alme, J., Barnaföldi, G.G., Barthel, R., Borshchov, V., Bodova, T., van den Brink, A., et al. <b>A High-Granularity Digital Tracking Calorimeter Optimized for Proton CT. </b> <i>Frontiers in Physics.</i>  2020;8(460).
** Published manuscript: [[Media:10.3389_fphy.2020.568243.pdf | PDF]]
** Frontiers link: [https://www.frontiersin.org/article/10.3389/fphy.2020.568243 doi:10.3389/fphy.2020.568243]
* Pettersen, H.E.S., Volz, L., Sølie, J. R., Alme, J., Barnaföldi, G.G., Barthel, R. et al. <b>Helium Radiography with a Digital Tracking Calorimeter-a Monte Carlo Study for Secondary Track Rejection. </b> <i> Phys. Med. Biol.</i> 2021;66(3):035004.
** Published manuscript: [[Media: Pettersen_2021_Phys._Med._Biol._66_035004.pdf | PDF]]
** IOP Science link: [https://iopscience.iop.org/article/10.1088/1361-6560/abca03 doi:10.1088/1361-6560/abca03]
* Sølie, J.R., Volz, L., Pettersen H.E.S., Piersimoni, P., Odland, O.H., Röhrich, D., et al. <b>Image quality of list-mode proton imaging without front trackers. </b> <i> Phys. Med. Biol.</i> 2020;65(13):135012.
** Published manuscript: [[Media: 10.1088_1361-6560_ab8.pdf | PDF]]
** IOP Science link: [https://iopscience.iop.org/article/10.1088/1361-6560/ab8ddb doi:10.1088/1361-6560/ab8ddb]
* Tambave, G., Alme, J., Barnaföldi, G.G., Barthel, R., Van Den Brink, A., Brons, S., et al.<b> Characterization of monolithic CMOS pixel sensor chip with ion beams for application in particle computed tomography. </b> <i> Nuclear Instruments and Methods in Physics Research Section A</i> 2020;958:162626.
** Published manuscript: [[Media: Tambave-2020-Characterization-of-monolithic-cm.pdf| PDF]]
** Elsevier link: [https://www.sciencedirect.com/science/article/pii/S0168900219311258?via%3Dihub doi:10.1016/j.nima.2019.162626]
* Pettersen, Helge Egil Seime, Johan Alme, Gergely Gabor Barnafoldi, Alba Garcıa-Santos, Ola Grøttvik, Håvard Helstrup, Kristin Fanebust Hetland, Ilker Meric, Odd Harald Odland, Gabor Papp, Thomas Peitzmann, Dieter Röhrich, Joao Seco, Hesam Shafiee, Eivind Vågslid Skjæveland, Ganesh Tambave, Kjetil Ullaland, Monika Varga-Kofarago, Lennart Volz, Boris Wagner and Shiming Yang. <b>Design Optimization of a Pixel Based Range Telescope for Proton Computed Tomography.</b> <i>Physica Medica Special Issue: Advances in Geant4 for medicine.</i> 2019; 63:87-97
** Published manuscript: [[Media: Pettersen et al. - Design Optimization of a Pixel Based Range Telesco.pdf| PDF]]
** Elsevier link: [https://www.sciencedirect.com/science/article/abs/pii/S1120179719301358 doi:10.1016/J.ejmp.2019.05.026 ]
* Pettersen, H.E.S., J. Alme, A. van den Brink, M. Chaar, D. Fehlker, I. Meric, O.H. Odland, et al. <b>Proton Tracking in a High-Granularity Digital Tracking Calorimeter for Proton CT Purposes</b>.  <i>Nuclear Instruments and Methods in Physics Research A 860C, 51–61. doi:10.1016/j.nima.2017.02.007.</i>
* Pettersen, H.E.S., J. Alme, A. van den Brink, M. Chaar, D. Fehlker, I. Meric, O.H. Odland, et al. <b>Proton Tracking in a High-Granularity Digital Tracking Calorimeter for Proton CT Purposes</b>.  <i>Nuclear Instruments and Methods in Physics Research A 860C, 51–61. doi:10.1016/j.nima.2017.02.007.</i>
** Published manuscript: [[Media: 1-s2.0-S0168900217301882-main.pdf | PDF]]
** Published manuscript: [[Media: 1-s2.0-S0168900217301882-main.pdf | PDF]]
Line 40: Line 97:
** [http://norskfysisk.no/filer/FFV/2017/FFV-2017-4.pdf Magazine at norskfysisk.no]
** [http://norskfysisk.no/filer/FFV/2017/FFV-2017-4.pdf Magazine at norskfysisk.no]


==== In review ====
==== Submitted ====
* Pettersen, H.E.S., Meric, I., Odland, O.H., Shafiee, H., Sølie, J., Röhrich, D. <b>Proton Tracking Algorithm for Pixel Based Range Telescopes for Proton Computed Tomography</b>. <i>Revision submitted to Web of Conferences after the "Connecting the Dots" conference.</i>
* Pettersen, H.E.S., Meric, I., Odland, O.H., Shafiee, H., Sølie, J., Röhrich, D. <b>Proton Tracking Algorithm for Pixel Based Range Telescopes for Proton Computed Tomography</b>. <i>Revision submitted to Web of Conferences after the "Connecting the Dots" conference.</i>
** Revised manuscript: [[Media: detector-proton-tracking.pdf | PDF]]
** Revised manuscript: [[Media: detector-proton-tracking.pdf | PDF]]
Line 47: Line 104:
** Submitted manuscript: [[Media: Authors manuscript.pdf | PDF]]
** Submitted manuscript: [[Media: Authors manuscript.pdf | PDF]]


* Pettersen, Helge Egil Seime, Johan Alme, Gergely Gabor Barnafoldi, Alba Garcıa-Santos, Ola Grøttvik, Håvard Helstrup, Kristin Fanebust Hetland, Ilker Meric, Odd Harald Odland, Gabor Papp, Thomas Peitzmann, Dieter Röhrich, Joao Seco, Hesam Shafiee, Eivind Vågslid Skjæveland, Ganesh Tambave, Kjetil Ullaland, Monika Varga-Kofarago, Lennart Volz, Boris Wagner and Shiming Yang. <b>Design Optimization of a Pixel Based Range Telescope for Proton Computed Tomography.</b> <i>Submitted to Physica Medica Special Issue: Advances in Geant4 for medicine.</i>
* Eikeland, Viljar Nilsen et al. <b> Bergen Proton CT System. </b> <i> Submitted as proceedings for the 12th Position Sensitive Detectors conference. </i>
** Submitted manuscript: [[Media: Pettersen et al. - Design Optimization of a Pixel Based Range Telesco.pdf| PDF]]
** Submitted manuscript: [[Media: psd_proceedings.pdf | PDF]]
 
==== Posters ====
* Eikeland, Viljar Nilsen. <b> Bergen proton CT system. </b> <i> Presented at the 12th Position Sensitive Detectors conference.</i>
** Submitted poster [[Media: poster_PSD12.pdf | PDF]]
 
 
 
== Meetings ==
Hosted on Indico  https://indico.cern.ch/category/13882.


==== Work in Progress ====
The old pages on the wiki can be found here: [[Meetings]]
* J. Sølie, H. E. S. Pettersen, I. Meric, O. H. Odland, H. Helstrup and D. Röhrich: <b>A comparison of longitudinal and lateral range for protons traversing complex media using GATE, MCNP6 and FLUKA Monte Carlo simulations</b>. <i>Rejected by Radiat. Phys. Chem. in conjunction with the [http://conferences.illinois.edu/irrma2017/ IRRMA X] conference.</i>
** Preliminary manuscript: [[Media: 1708.00668.pdf |PDF]]
** arXiv link: [https://arxiv.org/abs/1708.00668  arXiv:1708.00668]


== [[Meetings]] ==
Slides from the project [[Workshops | workshops in 2016]]
Notes and slides from the project meetings


== [[Workshops]] ==
== [[Commissioning]] ==
Slides from the project [[Workshops | workshops]]
Planning and information on [[Commissioning | commissioning, beam tests, etc]].


== [[Workpackages]] ==
== [[Workpackages]] ==
Sections for the different work packages
Sections for the different [[Workpackages | work packages]]


== [[People]] ==
== [[People]] ==

Latest revision as of 12:32, 14 March 2024

Wiki for the proton CT project

Documentation and Howto's

Software

  • Software Documentation on how to install and use the involved software packages, how to use the GitLab service, and about the development workflow, etc.

Hardware

Control & Readout Software

ALPIDE

Cooling

Cooling Documentation on the cooling simulations, measurements, laboratory setup and the final design.

Århus Testbeam 2023

Århus Testbeam 2023 Documentation on the testbeam at Århus hospital including simulation, setup, equipment used, etc.

Publications

List of publications from the project.

Workpackage Reports

Theses

Journal Articles

  • Alme, J., Barnaföldi, G.G., Barthel, R., Borshchov, V., Bodova, T., van den Brink, A., et al. A High-Granularity Digital Tracking Calorimeter Optimized for Proton CT. Frontiers in Physics. 2020;8(460).
  • Pettersen, H.E.S., Volz, L., Sølie, J. R., Alme, J., Barnaföldi, G.G., Barthel, R. et al. Helium Radiography with a Digital Tracking Calorimeter-a Monte Carlo Study for Secondary Track Rejection. Phys. Med. Biol. 2021;66(3):035004.
  • Sølie, J.R., Volz, L., Pettersen H.E.S., Piersimoni, P., Odland, O.H., Röhrich, D., et al. Image quality of list-mode proton imaging without front trackers. Phys. Med. Biol. 2020;65(13):135012.
  • Tambave, G., Alme, J., Barnaföldi, G.G., Barthel, R., Van Den Brink, A., Brons, S., et al. Characterization of monolithic CMOS pixel sensor chip with ion beams for application in particle computed tomography. Nuclear Instruments and Methods in Physics Research Section A 2020;958:162626.
  • Pettersen, Helge Egil Seime, Johan Alme, Gergely Gabor Barnafoldi, Alba Garcıa-Santos, Ola Grøttvik, Håvard Helstrup, Kristin Fanebust Hetland, Ilker Meric, Odd Harald Odland, Gabor Papp, Thomas Peitzmann, Dieter Röhrich, Joao Seco, Hesam Shafiee, Eivind Vågslid Skjæveland, Ganesh Tambave, Kjetil Ullaland, Monika Varga-Kofarago, Lennart Volz, Boris Wagner and Shiming Yang. Design Optimization of a Pixel Based Range Telescope for Proton Computed Tomography. Physica Medica Special Issue: Advances in Geant4 for medicine. 2019; 63:87-97
  • Pettersen, H.E.S., J. Alme, A. van den Brink, M. Chaar, D. Fehlker, I. Meric, O.H. Odland, et al. Proton Tracking in a High-Granularity Digital Tracking Calorimeter for Proton CT Purposes. Nuclear Instruments and Methods in Physics Research A 860C, 51–61. doi:10.1016/j.nima.2017.02.007.
  • Pettersen, H.E.S., Chaar, M., Meric, I., Odland, O.H., Sølie, J., Röhrich, D. Accuracy of parameterized proton range models; a comparison. Radiation Physics and Chemistry, 144 (C): 295-297 (2018). doi:10.1016/j.radphyschem.2017.08.02
  • Pettersen, H. E. S., and D. Röhrich. 2017. Kreftbehandling Med Protonterapi Og Proton CT. Fra Fysikkens Verden, December 2017.

Submitted

  • Pettersen, H.E.S., Meric, I., Odland, O.H., Shafiee, H., Sølie, J., Röhrich, D. Proton Tracking Algorithm for Pixel Based Range Telescopes for Proton Computed Tomography. Revision submitted to Web of Conferences after the "Connecting the Dots" conference.
    • Revised manuscript: PDF
  • Pettersen, Helge Egil Seime, Lennart Volz, Jarle Sølie, Dieter Rohrich, and Joao Seco. A Linear Projection Model to Estimate a Proton’s Position in a Pencil Beam For Single Sided Proton Imaging,. Submitted to Physics in Medicine and Biology.
    • Submitted manuscript: PDF
  • Eikeland, Viljar Nilsen et al. Bergen Proton CT System. Submitted as proceedings for the 12th Position Sensitive Detectors conference.
    • Submitted manuscript: PDF

Posters

  • Eikeland, Viljar Nilsen. Bergen proton CT system. Presented at the 12th Position Sensitive Detectors conference.
    • Submitted poster PDF


Meetings

Hosted on Indico https://indico.cern.ch/category/13882.

The old pages on the wiki can be found here: Meetings

Slides from the project workshops in 2016

Commissioning

Planning and information on commissioning, beam tests, etc.

Workpackages

Sections for the different work packages

People

Contact info of involved people

Links

Link collection of topics regarding the project

Getting started

  • Note: ASK is a placeholder that marks questions
  • Note: Search function is not ideal. It doesn't find all occurences of the search term, e.g. aries finds libraries but not aries.bccs
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