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1

Application of the compress sensing theory for improvement of the TOF resolution in a novel J-PET instrument

Raczyński L., Moskal P., Kowalski P., Wiślicki W., Bednarski T., Białas P., Czerwiński E., Gajos A., Kapłon Ł., Kochanowski A., Korcyl G., Kowal J., Kozik T., Krzemień W., Kubicz E., Niedźwiecki S., Pałka M., Rudy Z., Salabura P., Gupta-Sharma N., Silarski M., Słomski A., Smyrski J., Strzelecki A., Wieczorek A., Zieliński M., Zoń N.

Nukleonika

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2016

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Vol. 61, No. 1

35--39

EN

Nowadays, in positron emission tomography (PET) systems, a time of fl ight (TOF) information is used to improve the image reconstruction process. In TOF-PET, fast detectors are able to measure the difference in the arrival time of the two gamma rays, with the precision enabling to shorten signifi cantly a range along the line-of-response (LOR) where the annihilation occurred. In the new concept, called J-PET scanner, gamma rays are detected in plastic scintillators. In a single strip of J-PET system, time values are obtained by probing signals in the amplitude domain. Owing to compressive sensing (CS) theory, information about the shape and amplitude of the signals is recovered. In this paper, we demonstrate that based on the acquired signals parameters, a better signal normalization may be provided in order to improve the TOF resolution. The procedure was tested using large sample of data registered by a dedicated detection setup enabling sampling of signals with 50-ps intervals. Experimental setup provided irradiation of a chosen position in the plastic scintillator strip with annihilation gamma quanta.

2

An Overview of ATmega AVR Microcontrollers Used in Scientific Research and Industrial Applications

Kunikowski W., Czerwiński E., Olejnik P., Awrejcewicz J.

Pomiary Automatyka Robotyka

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2015

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R. 19, nr 1

15--19

EN

Nowadays, microcontrollers are commonly used in many fields of industrial applications previously dominated by other devices. Their strengths such as: processing power, low cost, and small sizes enable them to become substitutes for industrial PLC controllers, analog electronic circuits, and many more. In first part of this article an overview of the Atmel AVR microprocessor family can be found, alongside with many scientific and industrial applications. Second part of this article contains a detailed description of two implementations of ATmega644PA microprocessor. First one is a controller with PID regulation that supports a DC motor driver. Second one is a differential equation solver with 4-th order Runge-Kutta method implemented. It is used for solving a torsion pendulum dynamics. Finally, some general conclusions regarding the two presented implementations are made.

PL

W dzisiejszych czasach mikrokontrolery są często używane w miejscach poprzednio zdominowanych przez inne układy logiczne. Argumenty przemawiające za stosowaniem tych układów, takie jak: moc obliczeniowa, niski koszt i małe rozmiary, pozwalają na zastępowanie nimi przemysłowych sterowników PLC i innych elektronicznych układów analogowych. W pierwszej części artykułu przedstawiono przegląd dostępnych mikroprocesorów Atmel AVR, uwzględniając przykłady naukowych i przemysłowych zastosowań. Druga część zawiera szczegółowy opis dwóch implementacji procesora ATmega644PA, przeprowadzonych przez autorów pracy. Pierwsza przedstawia regulator PID silnika prądu stałego obciążonego zmiennym momentem. Kolejna przedstawia implementację metody Runge-Kutty czwartego rzędu, stosowanej często do rozwiązywania równań różniczkowych. Algorytm został zastosowany do rozwiązania zadania dynamiki ruchu obrotowego wahadła torsyjnego na mikrokontrolerze.

3

Studies of unicellular microorganisms Saccharomyces cerevisiae by means of positron annihilation lifetime spectroscopy

Kubicz E., Jasińska B., Zgardzińska B., Bednarski T., Białas P., Czerwiński E., Gajos A., Gorgol M., Kamińska D., Kapłon Ł., Kochanowski A., Korcyl G., Kowalski P., Kozik T., Krzemień W., Niedźwiecki S., Pałka M., Raczyński L., Rajfur Z., Rudy Z., Rundel O., Sharma N. G., Silarski M., Słomski A., Strzelecki A., Wieczorek A., Wiślicki W., Zieliński M., Moskal P.

Nukleonika

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2015

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Vol. 60, No. 4, part 1

749--753

EN

Results of positron annihilation lifetime spectroscopy (PALS) and microscopic studies on simple microorganisms, brewing yeasts, are presented. Lifetime of ortho-positronium (o-Ps) were found to change from 2.4 to 2.9 ns (longer-lived component) for lyophilized and aqueous yeasts, respectively. Also hygroscopicity of yeasts in time was examined, allowing to check how water – the main component of the cell – affects PALS parameters, thus lifetime of o-Ps were found to change from 1.2 to 1.4 ns (shorter-lived component) for the dried yeasts. The time sufficient to hydrate the cells was found below 10 hours. In the presence of liquid water, an indication of reorganization of yeast in the molecular scale was observed. Microscopic images of the lyophilized, dried, and wet yeasts with best possible resolution were obtained using inverted microscopy (IM) and environmental scanning electron microscopy (ESEM) methods. As a result, visible changes to the surface of the cell me mbrane were observed in ESEM images.

4

Searches for discrete symmetries violation in ortho-positronium decay using the J-PET detector

Kamińska D., Gajos A., Czerwiński E., Bednarski T., Białas P., Gorgol M., Jasińska B., Kapłon Ł., Korcyl G., Kowalski P., Kozik T., Krzemień W., Kubicz E., Niedźwiecki S., Pałka M., Raczyński L., Rudy Z., Rundel O., Sharma N. G., Silarski M., Słomski A., Strzelecki A., Wieczorek A., Wiślicki W., Zieliński M., Zgardzińska B., Moskal P.

Nukleonika

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2015

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Vol. 60, No. 4, part 1

729--732

EN

In this paper, we present prospects for using the Jagiellonian positron emission tomograph (J-PET) detector to search for discrete symmetries violations in a purely leptonic system of the positronium atom. We discuss tests of CP and CPT symmetries by means of ortho-positronium decays into three photons. No zero expectation values for chosen correlations between ortho-positronium spin and momentum vectors of photons would imply the existence of physics phenomena beyond the standard model. Previous measurements resulted in violation amplitude parameters for CP and CPT symmetries consistent with zero, with an uncertainty of about 10−3. The J-PET detector allows to determine those values with better precision, thanks to the unique time and angular resolution combined with a high geometrical acceptance. Achieving the aforementioned is possible because of the application of polymer scintillators instead of crystals as detectors of annihilation quanta.

5

Reconstruction of hit time and hit position of annihilation quanta in the J-PET detector using the Mahalanobis distance

Sharma N. G., Silarski M., Bednarski T., Białas P., Czerwiński E., Gajos A., Gorgol M., Jasińska B., Kamińska D., Kapłon Ł., Korcyl G., Kowalski P., Kozik T., Krzemień W., Kubicz E., Niedźwiecki S., Pałka M., Raczyński L., Rudy Z., Rundel O., Słomski A., Strzelecki A., Wieczorek A., Wiślicki W., Zieliński M., Zgardzińska B., Moskal P.

Nukleonika

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2015

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Vol. 60, No. 4, part 1

765--769

EN

The J-PET detector being developed at the Jagiellonian University is a positron emission tomograph composed of the long strips of polymer scintillators. At the same time, it is a detector system that will be used for studies of the decays of positronium atoms. The shape of photomultiplier signals depends on the hit time and hit position of the gamma quantum. In order to take advantage of this fact, a dedicated sampling front-end electronics that enables to sample signals in voltage domain with the time precision of about 20 ps and novel reconstruction method based on the comparison of examined signal with the model signals stored in the library has been developed. As a measure of the similarity, we use the Mahalanobis distance. The achievable position and time resolution depend on the number and values of the threshold levels at which the signal is sampled. A reconstruction method as well as preliminary results are presented and discussed.

6

Processing optimization with parallel computing for the J-PET scanner

Krzemień W., Bała M., Bednarski T., Białas P., Czerwiński E., Gajos A., Gorgol M., Jasińska B., Kamińska D., Kapłon Ł., Korcyl G., Kowalski P., Kozik T., Kubicz E., Niedźwiecki S., Pałka M., Raczyński L., Rudy Z., Rundel O., Sharma N. G., Silarski M., Słomski A., Stola K., Strzelecki A., Trybek D., Wieczorek A., Wiślicki W., Zieliński M., Zgardzińska B., Moskal P.

Nukleonika

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2015

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Vol. 60, No. 4, part 1

745--748

EN

The Jagiellonian Positron Emission Tomograph (J-PET) collaboration is developing a prototype time of flight (TOF)-positron emission tomograph (PET) detector based on long polymer scintillators. This novel approach exploits the excellent time properties of the plastic scintillators, which permit very precise time measurements. The very fast fi eld programmable gate array (FPGA)-based front-end electronics and the data acquisition system, as well as low- and high-level reconstruction algorithms were specially developed to be used with the J-PET scanner. The TOF-PET data processing and reconstruction are time and resource demanding operations, especially in the case of a large acceptance detector that works in triggerless data acquisition mode. In this article, we discuss the parallel computing methods applied to optimize the data processing for the J-PET detector. We begin with general concepts of parallel computing and then we discuss several applications of those techniques in the J-PET data processing.

7

PALS investigations of free volumes thermal expansion of J-PET plastic scintillator synthesized in polystyrene matrix

Wieczorek A., Zgardzińska B., Jasińska B., Gorgol M., Bednarski T., Białas P., Czerwiński E., Gajos A., Kamińska D., Kapłon Ł., Kochanowski A., Korcyl G., Kowalski P., Kozik T., Krzemień W., Kubicz E., Niedźwiecki S., Pałka M., Raczyński L., Rudy Z., Rundel O., Sharma N. G., Silarski M., Silarski A., Strzelecki A., Wiślicki W., Zieliński M., Moskal P.

Nukleonika

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2015

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Vol. 60, No. 4, part 1

777--781

EN

The polystyrene doped with 2,5-diphenyloxazole as a primary fluor and 2-(4-styrylphenyl)benzoxazole as a wavelength shifter prepared as a plastic scintillator was investigated using positronium probe in wide range of temperatures from 123 to 423 K. Three structural transitions at 260, 283, and 370 K were found in the material. In the o-Ps intensity dependence on temperature, the significant hysteresis is observed. Heated to 370 K, the material exhibits the o-Ps intensity variations in time.

8

Modeling and parameter identification of vibrations of a double torsion pendulum with friction

Czerwiński E., Olejnik P., Awrejcewicz J.

Acta Mechanica et Automatica

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2015

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Vol. 9, no. 4

204--212

EN

The purpose of this paper is to investigate a double torsion pendulum with planar frictional contact. The single torsion pendulum with one-degree-of-freedom is an angular equivalent of the linear harmonic oscillator. The second degree of freedom has been obtained by adding a free body to the inverted single torsion pendulum. The free body’s angular displacement is caused by frictional forces appearing in the interface (contact zone) between the free body and the pendulum column’s head kinematically excited at its base by a mechanism with torsion spiral spring. An experimental station has been set up and run to find most unknown parameters of the pendulum from the time series of state variables taken as inputs to the Nelder-Mead method of identification. The obtained results proved significant usability of the identification method in the case of numerical simulation of the pendulum’s dynamical model. It has not been satisfactorily proved in the case of time characteristics coming from a real system that exhibits also some unrecognized physical effects.

9

Trigger-less and reconfigurable data acquisition system for positron emission tomography

Korcyl G., Moskal P., Bednarski T., Białas P., Czerwiński E., Kapłon Ł., Kochanowski A., Kowal J., Kowalski P., Kozik T., Krzemień W., Molenda M., Niedźwiecki S., Pałka M., Pawlik M., Raczyński L., Rudy Z., Salabura P., Gupta-Sharma N., Silarski M., Słomski A., Smyrski J., Strzelecki A., Wiślicki W., Zieliński M., Zoń N.

Bio-Algorithms and Med-Systems

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2014

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Vol. 10, no. 1

37--40

EN

This article is focused on data acquisition system (DAQ) designed especially to be used in positron emission tomography (PET) or single-photon emission computed tomography. The system allows for continuous registration of analog signals during measurement. It has been designed to optimize registration and processing of the information carried by signals from the detector system in PET scanner. The processing does not require any rejection of data with a trigger system. The proposed system possesses also an ability to implement various data analysis algorithms that can be performed in real time during data collection.

10

Simulations of γ quanta scattering in a single module of the J-PET detector

Szymański K., Moskal P., Bednarski T., Białas P., Czerwiński E., Giergiel K., Kapłon Ł., Kochanowski A., Korcyl G., Kowal J., Kowalski P., Kozik T., Krzemień W., Molenda M., Moskal I., Niedźwiecki S., Pałka M., Pawlik-Niedźwiecka M., Raczyński L., Rudy Z., Salabura P., Gupta-Sharma N., Silarski M., Słomski A., Smyrski J., Strzelecki A., Witkowski P., Wiślicki W., Zieliński M., Zoń N.

Bio-Algorithms and Med-Systems

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2014

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Vol. 10, no. 2

71--77

EN

This article describes the simulations of the scattering of annihilation γ quanta in a strip of a plastic scintillator. Such strips constitute the basic detection modules in a newly proposed positron emission tomography (PET), which utilizes plastic scintillators instead of inorganic crystals. An algorithm simulating the chain of Compton scatterings was elaborated and a series of simulations have been conducted for the scintillator strip with a cross-section of 5×19 mm. The results indicate that secondary interactions occur only in the case of about 8% of the events and only 25% of these events take place in the distance larger than 0.5 cm from the primary interaction. Also, the light signals produced at the primary and secondary interactions overlap with the delay, the distribution of which is characterized by a full width at half-maximum (FWHM) of about 40 ps.

11

Plastic scintillators for positron emission tomography obtained by the bulk polymerization method

Kapłon Ł., Kochanowski A., Molenda M., Moskal P., Wieczorek A., Bednarski T., Białas P., Czerwiński E., Korcyl G., Kowal J., Kowalski P., Kozik T., Krzemień W., Niedźwiecki S., Pałka M., Pawlik M., Raczyński L., Rudy Z., Salabura P., Gupta-Sharma N., Silarski M., Słomski A., Smyrski J., Strzelecki A., Wiślicki W., Zieliński M., Zoń N.

Bio-Algorithms and Med-Systems

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2014

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Vol. 10, no. 1

27--31

EN

This paper describes three methods regarding the production of plastic scintillators. One method appears to be suitable for the manufacturing of plastic scintillators, revealing properties which fulfill the requirements of novel positron emission tomography scanners based on plastic scintillators. The key parameters of the manufacturing process are determined and discussed.

12

List-mode reconstruction in 2D strip PET

Białas P., Kowal J., Strzelecki A., Bednarski T., Czerwiński E., Giergiel K., Kapłon Ł., Kochanowski A., Korcyl G., Kowalski P., Kozik T., Krzemień W., Molenda M., Moskal I., Moskal P., Niedźwiecki S., Pałka M., Pawlik M., Raczyński L., Rudy Z., Salabura P., Gupta-Sharma N., Silarski M., Słomski A., Smyrski J., Szymański K., Wiślicki W., Witkowski P., Zieliński M., Zoń N.

Bio-Algorithms and Med-Systems

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2014

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Vol. 10, no. 1

9--12

EN

Using a theory of list-mode maximum likelihood expectation-maximization (MLEM) algorithm, in this contribution, we present a derivation of the system response kernel for a novel positron emission tomography (PET) detector based on plastic scintillators.

13

J-PET analysis framework for the prototype TOF-PET detector

Krzemień W., Silarski M., Stoła K., Trybek D., Bednarski T., Białas P., Czerwiński E., Kapłon Ł., Kochanowski A., Korcyl G., Kowal J., Kowalski P., Kozik T., Molenda M., Moskal P., Niedźwiecki S., Pałka M., Pawlik M., Raczyński L., Rudy Z., Salabura P., Gupta-Sharma N., Słomski A., Smyrski J., Strzelecki A., Wiślicki W., Zieliński M., Zoń N.

Bio-Algorithms and Med-Systems

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2014

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Vol. 10, no. 1

33--36

EN

Novel time-of-flight positron emission tomography (TOF-PET) scanner solutions demand, apart from the state-of-the-art detectors, software for fast processing of the gathered data, monitoring of the whole scanner, and reconstruction of the PET image. In this article, we present an analysis framework for the novel STRIP-PET scanner developed by the J-PET collaboration in the Institute of Physics of the Jagiellonian University. This software is based on the ROOT package used in many particle physics experiments.

14

Determination of the map of efficiency of the Jagiellonian Positron Emission Tomograph (J-PET) detector with the GATE package

Kowalski P., Raczyński L., Bednarski T., Białas P., Czerwiński E., Giergiel K., Kapłon Ł., Kochanowski A., Korcyl G., Kowal J., Kozik T., Krzemień W., Molenda M., Moskal I., Moskal P., Niedźwiecki S., Pałka M., Pawlik-Niedźwiecka M., Rudy Z., Salabura P., Gupta-Sharma N., Silarski M., Słomski A., Smyrski J., Strzelecki A., Szymański K., Wiślicki W., Witkowski P., Zieliński M., Zoń N.

Bio-Algorithms and Med-Systems

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2014

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Vol. 10, no. 2

85--90

EN

A novel PET detector consisting of strips of polymer scintillators is being developed by the Jagiellonian Positron Emission Tomograph (J-PET) collaboration. The map of efficiency and the map of geometrical acceptance of the two-strip J-PET scanner are presented. The map of efficiency was determined using the Monte Carlo simulation software GEANT4 Application for Tomographic Emission (GATE), which is based on GEANT4. Both maps were compared using a method based on the χ2-test.

15

Database and data structure for the novel TOF-PET detector developed for the J-PET project

Czerwiński E., Zieliński M., Bednarski T., Białas P., Kapłon Ł., Kochanowski A., Korcyl G., Kowal J., Kowalski P., Kozik T., Krzemień W., Kubicz E., Molenda M., Moskal P., Niedźwiecki S., Pałka M., Pawlik-Niedźwiecka M., Raczyński L., Rudy Z., Salabura P., Gupta-Sharma N., Silarski M., Słomski A., Smyrski J., Strzelecki A., Wieczorek A., Wiślicki W., Zoń N.

Bio-Algorithms and Med-Systems

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2014

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Vol. 10, no. 2

79--83

EN

The complexity of the hardware and the amount of data collected during the PET imaging process require application of modern methods of efficient data organization and processing. In this article, we will discuss the data structures and the flow of collected data from the novel TOF-PET medical scanner that is being developed at the Jagiellonian University. The developed data format reflects the registration process of the γ quanta emitted from positron electron annihilation, front-end electronic structure, and required input information for the image reconstruction. In addition, the system database fulfills possible demands of the evolving J-PET project.

16

Computing support for advanced medical data analysis and imaging

Wiślicki W., Bednarski T., Białas P., Czerwiński E., Kapłon Ł., Kochanowski A., Korcyl G., Kowal J., Kowalski P., Kozik T., Krzemień W., Molenda M., Moskal P., Niedźwiecki S., Pałka M., Pawlik-Niedźwiecka M., Raczyński L., Rudy Z., Salabura P., Gupta-Sharma N., Silarski M., Słomski A., Smyrski J., Strzelecki A., Wieczorek A., Zieliński M., Zoń N.

Bio-Algorithms and Med-Systems

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2014

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Vol. 10, no. 2

53--58

EN

We discuss computing issues for data analysis and image reconstruction of positron emission tomography based on time-of-flight medical scanner or other medical scanning devices producing large volumes of data. Service architecture based on grid and cloud concepts for distributed processing is proposed and critically discussed.

17

Calibration of photomultipliers gain used in the J-PET detector

Bednarski T., Czerwiński E., Moskal P., Białas P., Giergiel K., Kapłon Ł., Kochanowski A., Korcyl G., Kowal J., Kowalski P., Kozik T., Krzemień W., Molenda M., Moskal I., Niedźwiecki S., Pałka M., Pawlik M., Raczyński L., Rudy Z., Salabura P., Gupta-Sharma N., Silarski M., Słomski A., Smyrski J., Strzelecki A., Szymański K. J., Wiślicki W., Witkowski P., Zieliński M., Zoń N.

Bio-Algorithms and Med-Systems

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2014

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Vol. 10, no. 1

13--17

EN

Photomultipliers are commonly used in commercial PET scanner as devices that convert light produced in scintillator by gamma quanta from positron-electron annihilation into electrical signal. For proper analysis of obtained electrical signal, a photomultiplier gain curve must be known, since gain can be significantly different even between photomultipliers of the same model. In this article, we describe single photoelectron method used for photomultiplier calibration applied for J-PET scanner, a novel PET detector being developed at Jagiellonian University. A description of calibration method, an example of calibration curve, and a gain of few Hamamatsu R4998 photomultipliers are presented.

18

Application of WLS strips for position determination in strip PET tomograph based on plastic scintillators

Smyrski J., Moskal P., Bednarski T., Białas P., Czerwiński E., Kapłon Ł., Kochanowski A., Korcyl G., Kowal J., Kowalski P., Kozik T., Krzemień W., Molenda M., Niedźwiecki S., Pałka M., Pawlik-Niedźwiecka M., Raczyński L., Rudy Z., Salabura P., Gupta-Sharma N., Silarski M., Słomski A., Strzelecki A., Wiślicki W., Zieliński M., Zoń N.

Bio-Algorithms and Med-Systems

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2014

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Vol. 10, no. 2

59--63

EN

A method of the determination of a γ-quantum absorption point in a plastic scintillator block using a matrix of wavelength-shifting (WLS) strips is proposed. An application of this method for the improvement of position resolution in newly proposed positron emission tomography (PET) detectors based on plastic scintillators is presented. The method enables to reduce parallax errors in the reconstruction of images, which occurs in the presently used PET scanners.

19

A novel method for calibration and monitoring of time synchronization of TOF-PET scanners by means of cosmic rays

Silarski M., Czerwiński E., Bednarski T., Moskal P., Białas P., Kapłon Ł., Kochanowski A., Korcyl G., Kowal J., Kowalski P., Kozik T., Krzemień W., Molenda M., Niedźwiecki S., Pałka M., Pawlik M., Raczyński L., Rudy Z., Salabura P., Gupta-Sharma N., Słomski A., Smyrski J., Strzelecki A., Wiślicki W., Zieliński M., Zoń N.

Bio-Algorithms and Med-Systems

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2014

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Vol. 10, no. 1

19--25

EN

All of the present methods for calibration and monitoring of time-of-flight positron emission tomography (TOF-PET) scanner detectors utilize radioactive isotopes, such as 22Na or 68Ge, which are placed or rotate inside the scanner. In this article, we describe a novel method based on the cosmic rays application to the PET calibration and monitoring methods. The concept allows to overcome many of the drawbacks of the present methods and it is well suited for newly developed TOF-PET scanners with a large longitudinal field of view. The method enables also the monitoring of the quality of the scintillator materials and in general allows for the continuous quality assurance of the PET detector performance.

20

A novel method based solely on field programmable gate array (FPGA) units enabling measurement of time and charge of analog signals in positron emission tomography (PET)

Pałka M., Moskal P., Bednarski T., Białas P., Czerwiński E., Kapłon Ł., Kochanowski A., Korcyl G., Kowal J., Kowalski P., Kozik T., Krzemień W., Molenda M., Niedźwiecki S., Pawlik M., Raczyński L., Rudy Z., Salabura P., Gupta-Sharma N., Silarski M., Słomski A., Smyrski J., Strzelecki A., Wiślicki W., Zieliński M, Zoń N.

Bio-Algorithms and Med-Systems

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2014

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Vol. 10, no. 1

41--45

EN

This article presents an application of a novel technique for precise measurements of time and charge based solely on a field programmable gate array (FPGA) device for positron emission tomography (PET). The described approach simplifies electronic circuits, reduces the power consumption, lowers costs, merges front-end electronics with digital electronics, and also makes more compact final design. Furthermore, it allows to measure time when analog signals cross a reference voltage at different threshold levels with a very high precision of ~15 ps (rms) and thus enables sampling of signals in a voltage domain.