Papers by Szymon Niedźwiecki
Mathematical Biosciences and Engineering, 2023
In positron emission tomography (PET) studies, convolutional neural networks (CNNs) may be applie... more In positron emission tomography (PET) studies, convolutional neural networks (CNNs) may be applied directly to the reconstructed distribution of radioactive tracers injected into the patient's body, as a pattern recognition tool. Nonetheless, unprocessed PET coincidence data exist in tabular format. This paper develops the transformation of tabular data into $ n $-dimensional matrices, as a preparation stage for classification based on CNNs. This method explicitly introduces a nonlinear transformation at the feature engineering stage and then uses principal component analysis to create the images. We apply the proposed methodology to the classification of simulated PET coincidence events originating from NEMA IEC and anthropomorphic XCAT phantom. Comparative studies of neural network architectures, including multilayer perceptron and convolutional networks, were conducted. The developed method increased the initial number of features from 6 to 209 and gave the best precision results (79.8$ % $) for all tested neural network architectures; it also showed the smallest decrease when changing the test data to another phantom.
The purpose of the reported research is the elaboration of the method for construction of the cos... more The purpose of the reported research is the elaboration of the method for construction of the cost-effective whole-body single-bed positron emission tomography scanner enabling simultaneous PET/CT and PET/MR imaging. The Jagiellonian Positron Emission Tomograph (J-PET) is built out of 192 scintillator strips arranged axially in three layers forming a cylindrical diagnostic chamber with the diameter of 85 cm and axial field-of-view of 50 cm. The novelty of the concept lies in employing long strips of plastic scintillators instead of crystals as detectors of the annihilation quanta, and in using the timing of signals instead of their amplitudes for the reconstruction of Lines-of-Response. To take advantage of the superior timing properties of plastic scintillators a novel multi-voltage-threshold front-end electronics was developed allowing for sampling of signals in a voltage domain. An axial arrangement of long strips of plastic scintillators, and their small light attenuation allows us to make a TOF-PET scanner with a long axial field-of-view. The presented solution opens unique possibilities of combining PET with CT and PET with MRI for scanning the same part of a patient at the same time with both methods. The relative ease of the cost effective increase of the axial field-of-view makes the J-PET tomograph competitive with respect to the current commercial PET scanners as regards sensitivity and time resolution.
Physics in Medicine & Biology
Objective. The Jagiellonian positron emission tomography (J-PET) technology, based on plastic sci... more Objective. The Jagiellonian positron emission tomography (J-PET) technology, based on plastic scintillators, has been proposed as a cost effective tool for detecting range deviations during proton therapy. This study investigates the feasibility of using J-PET for range monitoring by means of a detailed Monte Carlo simulation study of 95 patients who underwent proton therapy at the Cyclotron Centre Bronowice (CCB) in Krakow, Poland. Approach. Discrepancies between prescribed and delivered treatments were artificially introduced in the simulations by means of shifts in patient positioning and in the Hounsfield unit to the relative proton stopping power calibration curve. A dual-layer, cylindrical J-PET geometry was simulated in an in-room monitoring scenario and a triple-layer, dual-head geometry in an in-beam protocol. The distribution of range shifts in reconstructed PET activity was visualized in the beam’s eye view. Linear prediction models were constructed from all patients in t...
arXiv (Cornell University), Apr 12, 2023
Background: Alongside the benefits of Total-Body imaging modalities, such as higher sensitivity, ... more Background: Alongside the benefits of Total-Body imaging modalities, such as higher sensitivity, single-bed position, low dose imaging, etc., their final construction cost prevents worldwide utilization. The main aim of this study is to present a simulation-based comparison of the sensitivities of existing and currently developed tomographs to introduce a cost-efficient solution for constructing a Total-Body PET scanner based on plastic scintillators. Methods: For the case of this study, eight tomographs based on the uEXPLORER configuration with different scintillator materials (BGO, LYSO), axial field-of-view (97.4 cm and 194.8 cm), and detector configuration (full and sparse) were simulated. In addition, 8 J-PET scanners with different configurations, such as various axial field-of-view (200 cm and 250 cm), the different cross-sections of plastic scintillator, and the multiple numbers of the plastic scintillator layers (2, 3, and 4), based on J-PET technology have been simulated by GATE software. Furthermore, Biograph Vision has been simulated to compare the results with standard PET scans. Two types of simulations have been performed. The first one with a centrally located source with a diameter of 1mm and a length of 250 cm, and the second one with the same source inside a water-filled cylindrical phantom with a diameter of 20 cm and a length of 183 cm. Results: With regards to sensitivity, among all the proposed scanners, the ones constructed with BGO crystals give the best performance (∼ 350 cps/kBq at the center). The utilization of sparse geometry or LYSO crystals significantly lowers the achievable sensitivity of such systems. The J-PET design gives a similar sensitivity to the sparse LYSO crystal-based detectors while having full detector coverage over the body. Moreover, it provides uniform sensitivity over the body with additional gain on its sides and provides the possibility for high-quality brain imaging. Conclusion: Taking into account not only the sensitivity but also the price of the Total-Body PET tomographs, which till now was one of the main obstacles in their widespread clinical availability, the J-PET tomography system based on plastic scintillators could be a cost-efficient alternative for Total-Body PET scanners.
arXiv (Cornell University), Feb 28, 2023
Objective: The aim of this work is to investigate the feasibility of the Jagiellonian Positron Em... more Objective: The aim of this work is to investigate the feasibility of the Jagiellonian Positron Emission Tomography (J-PET) scanner for intra-treatment proton beam range monitoring. Approach: The Monte Carlo simulation studies with GATE and PET image reconstruction with CASToR were performed in order to compare six J-PET scanner geometries (three dual-heads and three cylindrical). We simulated proton irradiation of a PMMA phantom with a Single Pencil Beam (SPB) and Spread-Out Bragg Peak (SOBP) of various ranges. The sensitivity and precision of each scanner were calculated, and considering the setup's cost-effectiveness, we indicated potentially optimal geometries for the J-PET scanner prototype dedicated to the proton beam range assessment. Main results: The investigations indicate that the double-layer cylindrical and triple-layer double-head configurations are the most promising for clinical application. We found that the scanner sensitivity is of the order of 10 −5 coincidences per primary proton, while the precision of the range assessment for both SPB and SOBP irradiation plans was found below 1 mm. Among the scanners with the same number of detector modules, the best results are found for the triple-layer dual-head geometry. Significance: We performed simulation studies demonstrating that the feasibility of the J-PET detector for PET-based proton beam therapy range monitoring is possible with reasonable sensitivity and precision enabling its pre-clinical tests in the clinical proton therapy environment. Considering the sensitivity, precision and costeffectiveness, the double-layer cylindrical and triple-layer dual-head J-PET geometry configurations seem promising for the future clinical application. Experimental tests are needed to confirm these findings.
Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment
IEEE Transactions on Radiation and Plasma Medical Sciences
We report a study of the original image reconstruction algorithm based on the time-of-flight maxi... more We report a study of the original image reconstruction algorithm based on the time-of-flight maximum likelihood expectation maximisation (TOF MLEM), developed for the total-body (TB) Jagiellonian PET (J-PET) scanners. The method is applicable to generic cylindrical or modular multi-layer layouts and is extendable to multi-photon imaging. The system response matrix (SRM) is repre
arXiv (Cornell University), Dec 5, 2022
Total-Body PET imaging is one of the most promising newly introduced modalities in the medical di... more Total-Body PET imaging is one of the most promising newly introduced modalities in the medical diagnostics. State-of-the-art PET scanners use inorganic scintillators such as L(Y)SO or BGO, however, those technologies The authors gratefully acknowledge the support of the Foundation for Polish Science through programme TEAM POIR.04.04.00-00-4204/17; the National Science Centre of Poland through grant nos.
EPJ Web of Conferences
The SIDDHARTA-2 experiment aims to perform the first measurement of the kaonic deuterium 2p → 1s ... more The SIDDHARTA-2 experiment aims to perform the first measurement of the kaonic deuterium 2p → 1s x-ray transition energy. Such measurement, together with the measurement of kaonic hydrogen 2p → 1s x-ray energy transition performed by the SIDDHARTA experiment in 2011, allows the determination of kaon proton and kaon neutron scattering lengths and represents a fundamental input for the low energies QCD in the strangeness sector theory. The SIDDHARTA-2 experiment is presently installed at the DAΦNE electronpositron collider at the National Laboratories of Frascati, in Italy. In May 2022, the kaonic 4He x-ray transitions measurement was performed by the complete SIDDHARTA-2 setup, by using a gaseous target. The result of this measurement is presented in this paper, with a specific focus on the background rejection performed by the kaon trigger system.
IEEE Transactions on Radiation and Plasma Medical Sciences
The growing interest in human-grade total body positron emission tomography (PET) systems has als... more The growing interest in human-grade total body positron emission tomography (PET) systems has also application in small animal research. Due to the existing limitations in human-based studies involving drug development and novel treatment monitoring, animal-based research became a necessary step for testing and protocol preparation. In this simulation-based study two unconventional, cost-effective small animal total body PET scanners (for mouse and rat studies) have been investigated in order to inspect their feasibility for preclinical research. They were designed with the novel technology explored by the Jagiellonian-PET (J-PET) Collaboration. Two main PET characteristics: sensitivity and spatial resolution were mainly inspected to evaluate their performance. Moreover, the impact of the scintillator dimension and time-of-flight on the latter parameter was
Physics in Medicine & Biology
Objective.This paper reports on the implementation and shows examples of the use of theProTheRaMo... more Objective.This paper reports on the implementation and shows examples of the use of theProTheRaMonframework for simulating the delivery of proton therapy treatment plans and range monitoring using positron emission tomography (PET).ProTheRaMonoffers 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 theProTheRaMonframework 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.TheProTheRaMonframework is based on GATE Monte Carlo software, theCASToRreconstruction 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 us...
Il Nuovo Cimento C, 2021
Low energy kaon-nuclei interaction at DAΦNE: The SIDDHARTA-2 experiment M. Miliucci(1)(∗), M. Baz... more Low energy kaon-nuclei interaction at DAΦNE: The SIDDHARTA-2 experiment M. Miliucci(1)(∗), M. Bazzi(), D. Bosnar(), M. Bragadireanu(), M. Carminati(), M. Cargnelli(), A. Clozza(), C. Curceanu(), G. Deda(), L. De Paolis(), R. Del Grande()()(), C. Fiorini(), C. Guaraldo(), M. Iliescu(), M. Iwasaki(), P. King(), P. Levi Sandri(), J. Marton(), P. Moskal(), F. Napolitano(), S. Niedźwiecki(), K. Piscicchia()(), A. Scordo(), F. Sgaramella()(), H. Shi()(), M. Silarski(), D. Sirghi()(), F. Sirghi()(), M. Skurzok()(), A. Spallone(), M. Tüchler(), O. Vazquez Doce()() and J. Zmeskal() () INFN-LNF, Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali di Frascati Frascati (Roma), Italy () Department of Physics, Faculty of Science, University of Zagreb Zagreb, Croatia () Horia Hulubei National Insititute of Physics and Nuclear Engineering (IFIN-HH) Magurele, Romania () Politecnico di Milano, Dipartimento di Elettronica, Informazione e Bioingegneria and INFN Sezione di Milano Milano, Italy (...
Physics in Medicine & Biology, 2021
The purpose of the presented research is estimation of the performance characteristics of the eco... more The purpose of the presented research is estimation of the performance characteristics of the economic total-body Jagiellonian-PET system (TB-J-PET) constructed from plastic scintillators. The characteristics are estimated according to the NEMA NU-2-2018 standards utilizing the GATE package. The simulated detector consists of 24 modules, each built out of 32 plastic scintillator strips (each with cross section of 6 mm times 30 mm and length of 140 or 200 cm) arranged in two layers in regular 24-sided polygon circumscribing a circle with the diameter of 78.6 cm. For the TB-J-PET with an axial field-of-view (AFOV) of 200 cm, a spatial resolutions (SRs) of 3.7 mm (transversal) and 4.9 mm (axial) are achieved. The noise equivalent count rate (NECR) peak of 630 kcps is expected at 30 kBq cc−1. Activity concentration and the sensitivity at the center amounts to 38 cps kBq−1. The scatter fraction (SF) is estimated to 36.2 %. The values of SF and SR are comparable to those obtained for the ...
2016 IEEE Nuclear Science Symposium, Medical Imaging Conference and Room-Temperature Semiconductor Detector Workshop (NSS/MIC/RTSD), 2016
The commercial Positron Emission Tomography (PET) scanners use inorganic crystal scintillators fo... more The commercial Positron Emission Tomography (PET) scanners use inorganic crystal scintillators for the detection of gamma photons. The Jagiellonian-PET (J-PET) detector exhibits high time resolution due to use of fast plastic scintillators and dedicated electronics circuits. Since the time resolution of PET scanner is influenced by numerous factors, e.g. a type of photomultipliers attached to the scintillators, the optimal selection of components of the J-PET system requires detailed understanding of the method for calculation the time resolution. In this paper we show the idea of this method, based on statistical analysis of the observed signals on the photomultiplier's output. The method is tested using signals registered by means of the single detection module of the J-PET scanner built out from 30 cm long plastic scintillator strips. We investigate two main factors affecting the photon registration probability, photomultipliers quantum efficiency and photomultipliers transit...
Here, positronium imaging is presented to determine cardiac myxoma (CM) extracted from patients u... more Here, positronium imaging is presented to determine cardiac myxoma (CM) extracted from patients undergoing urgent cardiac surgery due to unexpected atrial masses. Positronium is an atom build from an electron and a positron, produced copiously in intra-molecular voids during the PET imaging. CM, the most common cardiac tumor in adults, accounts for 50-75% of benign cardiac tumors. We aimed to assess if positronium serves as a biomarker for diagnosing CM. Perioperative examinations and histopathology staining in six patients confirmed the primary diagnosis of CM. We observed significant differences in the mean positronium lifetime between tumor and normal tissues, with an average value of 1.92(02) ns and 2.72(05) ns for CM and the adipose tissue, respectively. Our findings, combined with positronium lifetime imaging, reveals the novel emerging positronium biomarker for cardiovascular imaging.One-Sentence SummaryPositronium may serve as an imaging biomarker for cancer diagnostics.
Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 2021
The J-PET tomograph is constructed from plastic scintillator strips arranged axially in concentri... more The J-PET tomograph is constructed from plastic scintillator strips arranged axially in concentric cylindrical layers. It enables investigations of positronium decays by measurement of the time, position, polarization and energy deposited by photons in the scintillators, in contrast to studies conducted so far with crystal and semiconductor based detection systems where the key selection of events is based on the measurement of the photons' energies. In this article we show that the J-PET tomograph system is capable of exclusive measurements of the decays of ortho-positronium atoms. We present the first positronium production results, its lifetime distribution measurements and discuss estimation of the influence of various background sources. The tomograph's performance demonstrated here makes it suitable for precision studies of positronium decays including entanglement of the final state photons, positron annihilation lifetime spectroscopy plus molecular imaging diagnostics.
Hyperfine Interactions, 2019
J-PET is the first positron-emission tomograph (PET) constructed from plastic scintillators. It w... more 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.
Hyperfine Interactions, 2018
The Jagiellonian Positron Emission Tomograph (J-PET) is a novel device being developed at Jagiell... more 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 (M. Mohammed) has been affiliated to affiliation 6. Please check if correct, otherwise, provide the correct affiliation.and high acceptance scanner that can be used as a multipurpose 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.
Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 2017
We demonstrated the feasibility of measuring the axial coordinate of a gamma quantum interaction ... more We demonstrated the feasibility of measuring the axial coordinate of a gamma quantum interaction point in a plastic scintillator bar via the detection of scintillation photons escaping from the scintillator with an array of wavelengthshifting (WLS) strips. Using a test setup comprising a BC-420 scintillator bar and an array of sixteen BC-482A WLS strips we achieved a spatial resolution of 5 mm (σ) for annihilation photons from a 22 Na isotope. The studied method can be used to improve the spatial resolution of a plastic-scintillator-based PET scanner which is being developed by the J-PET collaboration.
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Papers by Szymon Niedźwiecki