Marian Smoluchowski
Institute of Physics

Jagiellonian University

Diploma thesis

Adaptation of image reconstruction algorithms with time-of-flight for the J-PET tomography scanner

Supervisor: dr Wojciech Krzemień

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Defence year: 2019

The main aim of this thesis is the implementation of various analytic image reconstruction algorithms in the frame of the J-PET Framework analysis package. The implemented algorithms: Kernel Density Estimation, Filtered Back-Projection and Time-Of-Flight-Filtered Back-Projection have been tested both using Monte Carlo simulations and experimental data gathered by the scanner. Obtained results show that the implemented algorithms reconstruct correctly the shape of the phantoms. Comparison studies between implemented algorithms have been performed. In reconstruction of the NEMA phantom, the best results have been obtained using the Shepp-Logan filter with the cut-off parametr equal to 0.75 of Nyquist frequency (corresponding to the Background Variability of 0.13 and the Contrast Recovery Coefficient equal to 1.03 for high activity region of radius 22 mm). For the Time of-Fligth Filtered Back-Projection algorithm, the best reconstruction was obtained using the Hamming filter with the cut-off parameter equal to Nyquist frequency (corresponding to the Background Variability of 0.17 and the Contrast Recovery Coefficient equal to 0.96 for high activity region of radius 22 mm).

Publications

ARTICLES POSTERS

1. 3D TOF-PET image reconstruction using total variation regularization
   L. Raczyński, W. Wiślicki, K. Klimaszewski, W. Krzemień, P. Kopka, P. Kowalski, R. Y. Shopa, M. Bała, J. Chhokar, C. Curceanu, E. Czerwinski, K. Dulski, J. Gajewski, A. Gajos, M. Gorgol, R. Del Grande, B. Hiesmayr, B. Jasińska, K. Kacprzak, L. Kapłon, D. Kisielewska, G. Korcyl, T. Kozik, N. Krawczyk, E. Kubicz, M. Mohammed, S. Niedźwiecki, M. Pałka, M. Pawlik-Niedźwiecka, J. Raj, K. Rakoczy, A. Ruciński, S. Sharma, S. Shivani, M. Silarski, M. Skurzok, E.Ł. Stepień, B. Zgardzińska, P. Moskal
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   Physica Medica 80 (2020) 230-242
   In this paper we introduce a semi-analytic algorithm for 3-dimensional image reconstruction for positron emission tomography (PET). The method consists of the back-projection of the acquired data into the most likely image voxel according to time-of-flight (TOF) information, followed by the filtering step in the image space using an iterative optimization algorithm with a total variation (TV) regularization. TV regularization in image space is more computationally efficient than usual iterative optimization methods for PET reconstruction with a full system matrix that uses TV regularization. The efficiency comes from the one-time TOF back-projection step that might also be described as a reformatting of the acquired data. An important aspect of our work concerns the evaluation of the filter operator of the linear transform mapping an original radioactive tracer distribution into the TOF back-projected image. We obtain concise, closed-form analytical formula for the filter operator. The proposed method is validated with the Monte Carlo simulations of the NEMA IEC phantom using a one-layer, 50 cm-long cylindrical device called Jagiellonian PET scanner. The results show a better image quality compared with the reference TOF maximum likelihood expectation maximization algorithm.
2. J-PET Framework: Software platform for PET tomography data reconstruction and analysis
   W. Krzemień, A. Gajos, K. Kacprzak, K. Rakoczy, G. Korcyl
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   SoftwareX 11 (2020) 100487

   HEP: arXiv:2002.10183
   J-PET Framework is an open-source software platform for data analysis, written in C++ and based on the ROOT package. It provides a common environment for implementation of reconstruction, calibration and filtering procedures, as well as for user-level analyses of Positron Emission Tomography data. The library contains a set of building blocks that can be combined by users with even little programming experience, into chains of processing tasks through a convenient, simple and well-documented API. The generic input-output interface allows processing the data from various sources: low-level data from the tomography acquisition system or from diagnostic setups such as digital oscilloscopes, as well as high-level tomography structures e.g. sinograms or a list of lines-of-response. Moreover, the environment can be interfaced with Monte Carlo simulation packages such as GEANT and GATE, which are commonly used in the medical scientific community.
3. Simulation studies of annihilation-photon's polarisation via Compton scattering with the J-PET tomograph
   N. Krawczyk, B.C. Hiesmayr, J. Chhokar, C. Curceanu, E. Czerwiński, K. Dulski, A. Gajos, M. Gorgol, N. Gupta-Sharma, B. Jasińska, D. Kisielewska, G. Korcyl, P. Kowalski, W. Krzemień, T. Kozik, E. Kubicz, M. Mohammed, Sz. Niedźwiecki, M. Pałka, M. Pawlik-Niedźwiecka, L. Raczyński, J. Raj, K. Rakoczy, Z. Rudy, S. Sharma, Shivani, R.Y. Shopa, M. Silarski, M. Skurzok, W. Wiślicki, B. Zgardzińska, M. Zieliński, P. Moskal
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   Hyperfine Interact. 240 (2019) 81

   HEP: arXiv:1901.06204
   J-PET is the first positron-emission tomograph (PET) constructed from plastic scintillators. It was optimized for the detection of photons from electron-positron annihilation. Such photons, having an energy of 511 keV, interact with electrons in plastic scintillators predominantly via the Compton effect. Compton scattering is at most probable at an angle orthogonal to the electric field vector of the interacting photon. Thus registration of multiple photon scatterings with J-PET enables to determine the polarization of the annihilation photons. In this contribution we present estimates on the physical limitation in the accuracy of the polarization determination of 511 keV photons with the J-PET detector.
4. A feasibility study of the time reversal violation test based on polarization of annihilation photons from the decay of ortho-Positronium with the J-PET detector
   J. Raj, A. Gajos, C. Curceanu, E. Czerwiński, K. Dulski, M. Gorgol, N. Gupta-Sharma, B. C. Hiesmayr, B. Jasińska, K. Kacprzak, Ł. Kapłon, D. Kisielewska, K. Klimaszewski, G. Korcyl, P. Kowalski, T. Kozik, N. Krawczyk, W. Krzemień, E. Kubicz, M. Mohammed, Sz. Niedźwiecki, M. Pałka, M. Pawlik-Niedźwiecka, L. Raczyński, K. Rakoczy, Z. Rudy, S. Sharma, Shivani, R.Y. Shopa, M. Silarski, M. Skurzok, W. Wiślicki, B. Zgardzińska, P. Moskal
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   Hyperfine Interact. 239 (2018) 56

   HEP: arXiv:1809.00847
   The Jagiellonian Positron Emission Tomograph (J-PET) is a novel device being developed at Jagiellonian University in Krakow, Poland based on organic scintillators. J-PET is an axially symmetric and high acceptance scanner that can be used as a multi-purpose detector system. It is well suited to pursue tests of discrete symmetries in decays of positronium in addition to medical imaging. J-PET enables the measurement of both momenta and the polarization vectors of annihilation photons. The latter is a unique feature of the J-PET detector which allows the study of time reversal symmetry violation operator which can be constructed solely from the annihilation photons momenta before and after the scattering in the detector.
5. Commissioning of the J-PET detector in view of the positron annihilation lifetime spectroscopy
   K. Dulski, C. Curceanu, E. Czerwiński, A. Gajos, M. Gorgol, N. Gupta-Sharma, B. C. Hiesmayr, B. Jasińska, K. Kacprzak, Ł. Kapłon, D. Kisielewska, K. Klimaszewski, G. Korcyl, P. Kowalski, N. Krawczyk, W. Krzemień, T. Kozik, E. Kubicz, M. Mohammed, Sz. Niedźwiecki, M. Pałka, M. Pawlik-Niedźwiecka, L. Raczyński, J. Raj, K. Rakoczy, Z. Rudy, S. Sharma, Shivani, R. Y. Shopa, M. Silarski, M. Skurzok, W. Wiślicki, B. Zgardzińska, P. Moskal
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   Hyperfine Interact. 239 (2018) 40

   HEP: arXiv:1809.05175
   The Jagiellonian Positron Emission Tomograph (J-PET) is the first PET device built from plastic scintillators. It is a multi-purpose detector designed for medical imaging and for studies of properties of positronium atoms in porous matter and in living organisms. In this article we report on the commissioning of the J-PET detector in view of studies of positronium decays. We present results of analysis of the positron lifetime measured in the porous polymer. The obtained results prove that J-PET is capable of performing simultaneous imaging of the density distribution of annihilation points as well as positron annihilation lifetime spectroscopy.
6. Estimating the NEMA characteristics of the J-PET tomograph using the GATE package
   P. Kowalski, W. Wiślicki, R.Y. Shopa, L. Raczyński, K. Klimaszewski, C. Curcenau, E. Czerwiński, K. Dulski, A. Gajos, M. Gorgol, N. Gupta-Sharma, B. Hiesmayr, B. Jasińska, Ł. Kapłon, D. Kisielewska-Kamińska, G. Korcyl, T. Kozik, W. Krzemień, E. Kubicz, M. Mohammed, S. Niedźwiecki, M. Pałka, M. Pawlik-Niedźwiecka, J. Raj, K. Rakoczy, Z. Rudy, S. Sharma, S. Shivani, M. Silarski, M. Skurzok, B. Zgardzińska, M. Zieliński, P. Moskal
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   abstract

   Phys. Med. Biol. 63 (2018) 165008

   HEP: arXiv:1808.00241
   A novel whole-body positron emission tomography (PET) system based on plastic scintillators is developed by the J-PET Collaboration. It consists of plastic scintillator strips arranged axially in the form of a cylinder, allowing the cost-effective construction of the total-body PET system. In order to determine the properties of the scanner prototype and optimize its geometry, advanced computer simulations were performed using the GATE (Geant4 application for tomographic emission) software. The spatial resolution, sensitivity, scatter fraction and noise equivalent count rate were estimated according to the National Electrical Manufacturers Association norm, as a function of the length of the tomograph, the number of detection layers, the diameter of the tomographic chamber and for various types of applied readout. For the single-layer geometry with a diameter of 85 cm, a strip length of 100 cm, a cross-section of 4 mm × 20 mm and silicon photomultipliers with an additional layer of wavelength shifter as the readout, the spatial resolution (full width at half maximum) in the centre of the scanner is equal to 3 mm (radial, tangential) and 6 mm (axial). For the analogous double-layer geometry with the same readout, diameter and scintillator length, with a strip crosssection of 7 mm × 20 mm, a noise equivalent count rate peak of 300 kcps was reached at 40 kBq cc?1 activity concentration, the scatter fraction is estimated to be about 35% and the sensitivity at the centre amounts to 14.9 cps kBq?1. Sensitivity profiles were also determined.

1. Towards molecular in-vivo cancer imaging by means of positronium and the J-PET tomograph
   P. Moskal, M. Bała, Z. Bura, J.Chhokar, M. Dadgar, K. Dulski, K.Farbaniec, A. Gajos, B. Jasińska, H. Karimi, E. Kubicz, G. Korcyl, K. Rakoczy, S. Sharma, E.Stępień
   FNP IIIrd Inter Deciplinary Congress meeting, April 11, 2019, Warsaw, Poland

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