J-PET Framework: Software platform for PET tomography data reconstruction and analysis

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.Comment: 14 pages, 5 figure

Estimating the NEMA characteristics of the J-PET tomograph using the GATE package

The novel whole-body 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. In order to determine properties of the scanner prototype and optimize its geometry, advanced computer simulations using the GATE software were performed. The spatial resolution, the sensitivity, the scatter fraction and the noise equivalent count rate were estimated according to the NEMA norm as a function of the length of the tomograph, number of the detection layers, diameter of the tomographic chamber and for various types of the applied readout. For the single-layer geometry with the diameter of 85 cm, strip length of 100 cm, cross-section of 4 mm x 20 mm and silicon photomultipliers with the additional layer of wavelength shifter as the readout, the spatial resolution (FWHM) 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 the strip cross-section of 7 mm x 20 mm, the NECR peak of 300 kcps was reached at 40 kBq/cc activity concentration, the scatter fraction is estimated to about 35% and the sensitivity at the centre amounts to 14.9 cps/kBq. Sensitivity profiles were also determined

Commissioning of the J-PET detector in view of the positron annihilation lifetime spectroscopy

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

Adaptacja algorytmów rekonstrukcji obrazu z uwzględnieniem czasu lotu dla tomografu J-PET

Głównym celem pracy jest zaimplementowanie analitycznych algorytmów rekonstrukcji obrazu w ramach pakietu oprogramowania J-PET. Zaimplementowane algorytmy: Kernel Density Estimation, Filtered Back-Projection and Time-Of-Flight-Filtered Back-Projection zostały przetestowane używając symulacji Monte Carlo, a także danych eksperymentalnych zarejestrowanych prototypem skanera J-PET. Przedstawione wyniki pokazują, że algorytmy rekonstruują poprawnie kształt fantomów. Dokonano studiów porównawczych zaimplementowanych algorytmów. Rekonstruując fantom NEMA, najlepsze wyniki zostały osiągnięte używając filtru Sheppa-Logana z parametrem częstotliwości odcięcia równym 0.75 częstotliwości Nyquista (Wariancja tła = 0.13, Kontrast obrazu = 1.03 dla obszaru kuli o wysokiej aktywności o promieniu 22 mm). Używając algorytmu Time-of-Fligth Filtered Back-Projection najlepszy wynik osiągnięto dla filtru Hamminga z parametrem częstotliwości odcięcia równym częstotliwości Nyquista (Wariancja tła = 0.17, Kontrast obrazu = 0.96 dla obszaru kuli o wysokiej aktywności o promieniu 22 mm).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)

Rozwój wyświetlacza zdarzeń oraz adaptacja algorytmów rekonstrukcji obrazu do tomografu J-PET

Głównym celem pracy jest stworzenie aplikacji umożliwiającej wizualizację danych z różnych etapów analizy i rekonstrukcji obrazu w tomografie PET. Ta aplikacja, o nazwie Event Display, udostępnia narzędzia dla naukowców i developerów pracującymi nad algorytmami i analizą danych do tomografu Jagiellonian PET (J-PET). W Event Display są dostępne 4 różne widoki: 1) widok 3D tomografu, 2) rozwinięty widok poszczególnych warstw scyntylatorów i 4) widok wyświetlający diagramy sygnałów zarejestrowanych na każdym z aktywnych fotopowielaczy. Druga część pracy jest poświęcona implementacji podstawowej wersji algorytmu filtrowanej projekcji wstecznej (FBP) w ramach pakietu oprogramowania J-PET. Zarówno Event Display jak i FBP zostały napisane używając języka c++ z zachowaniem obiektowego wzorca programowania. Event Display używa także niektórych bibliotek z pakietu ROOT w celu stworzenia interfejsu graficznego i wizualizacji tomografu w 3D.The main aim of this thesis is to develop a program for data visualization at different stages of the PET data analysis and reconstruction. This application called Event Display, provides tools for scientists and developers working on the various algorithms and data analyses for the Jagiellonian PET scanner (J-PET). The Event Display implements four different data views: 1) 3D scanner view, 2) unrolled view, 3) front view and finally 4) diagram view. Second part of the thesis is devoted to the implementation of the basic Filtered Back-Projection algorithm in the frame of the J-PET software package. The Event Display and Filtered Back-Projection algorithms have been developed with c++ language using object-oriented design. The Event Display uses some of the ROOT package libraries for the development of graphical user interface and visualize the geometry of the detector

3D TOF-PET image reconstruction using total variation regularization

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 full system matrix that use 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