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  1. Book ; Online: Additional Look into GAN-based Augmentation for Deep Learning COVID-19 Image Classification

    Fedoruk, Oleksandr / Klimaszewski, Konrad / Ogonowski, Aleksander / Kruk, Michał

    2024  

    Abstract: The availability of training data is one of the main limitations in deep learning applications for medical imaging. Data augmentation is a popular approach to overcome this problem. A new approach is a Machine Learning based augmentation, in particular ... ...

    Abstract The availability of training data is one of the main limitations in deep learning applications for medical imaging. Data augmentation is a popular approach to overcome this problem. A new approach is a Machine Learning based augmentation, in particular usage of Generative Adversarial Networks (GAN). In this case, GANs generate images similar to the original dataset so that the overall training data amount is bigger, which leads to better performance of trained networks. A GAN model consists of two networks, a generator and a discriminator interconnected in a feedback loop which creates a competitive environment. This work is a continuation of the previous research where we trained StyleGAN2-ADA by Nvidia on the limited COVID-19 chest X-ray image dataset. In this paper, we study the dependence of the GAN-based augmentation performance on dataset size with a focus on small samples. Two datasets are considered, one with 1000 images per class (4000 images in total) and the second with 500 images per class (2000 images in total). We train StyleGAN2-ADA with both sets and then, after validating the quality of generated images, we use trained GANs as one of the augmentations approaches in multi-class classification problems. We compare the quality of the GAN-based augmentation approach to two different approaches (classical augmentation and no augmentation at all) by employing transfer learning-based classification of COVID-19 chest X-ray images. The results are quantified using different classification quality metrics and compared to the results from the literature. The GAN-based augmentation approach is found to be comparable with classical augmentation in the case of medium and large datasets but underperforms in the case of smaller datasets. The correlation between the size of the original dataset and the quality of classification is visible independently from the augmentation approach.

    Comment: Submitted to Machine Graphics & Vision
    Keywords Electrical Engineering and Systems Science - Image and Video Processing ; Computer Science - Computer Vision and Pattern Recognition ; I.5
    Subject code 006
    Publishing date 2024-01-26
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online: Performance of GAN-based augmentation for deep learning COVID-19 image classification

    Fedoruk, Oleksandr / Klimaszewski, Konrad / Ogonowski, Aleksander / Możdżonek, Rafał

    2023  

    Abstract: The biggest challenge in the application of deep learning to the medical domain is the availability of training data. Data augmentation is a typical methodology used in machine learning when confronted with a limited data set. In a classical approach ... ...

    Abstract The biggest challenge in the application of deep learning to the medical domain is the availability of training data. Data augmentation is a typical methodology used in machine learning when confronted with a limited data set. In a classical approach image transformations i.e. rotations, cropping and brightness changes are used. In this work, a StyleGAN2-ADA model of Generative Adversarial Networks is trained on the limited COVID-19 chest X-ray image set. After assessing the quality of generated images they are used to increase the training data set improving its balance between classes. We consider the multi-class classification problem of chest X-ray images including the COVID-19 positive class that hasn't been yet thoroughly explored in the literature. Results of transfer learning-based classification of COVID-19 chest X-ray images are presented. The performance of several deep convolutional neural network models is compared. The impact on the detection performance of classical image augmentations i.e. rotations, cropping, and brightness changes are studied. Furthermore, classical image augmentation is compared with GAN-based augmentation. The most accurate model is an EfficientNet-B0 with an accuracy of 90.2 percent, trained on a dataset with a simple class balancing. The GAN augmentation approach is found to be subpar to classical methods for the considered dataset.

    Comment: To be published in prceedings of WMLQ2022 International Workshop on Machine Learning and Quantum Computing Applications in Medicine and Physics
    Keywords Electrical Engineering and Systems Science - Image and Video Processing ; Computer Science - Computer Vision and Pattern Recognition ; Physics - Medical Physics ; I.5
    Subject code 006
    Publishing date 2023-04-18
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Can we enhance amphibians' habitat restoration in the post-mining areas?

    Klimaszewski, Krzysztof / Pacholik, Ewa / Snopek, Adam

    Environmental science and pollution research international

    2016  Volume 23, Issue 17, Page(s) 16941–16945

    Abstract: The study was aimed to evaluate the selected improvements of nature restoration in a depleted gravel pit. The study site consisted of four water reservoirs of different shapes and sizes, flooded after the gravel extraction ended. Ecological succession ... ...

    Abstract The study was aimed to evaluate the selected improvements of nature restoration in a depleted gravel pit. The study site consisted of four water reservoirs of different shapes and sizes, flooded after the gravel extraction ended. Ecological succession monitoring, conducted by the Warsaw University of Life Sciences students associated in the Student Scientific Association of Animal Sciences Faculty since the completion of mining, have focused on amphibians. A twofold approach upheld amphibian species population dynamics, as well as selected habitat elements. The restoration practices dedicated to habitat conditions enhancing have been proved to be definitely effective and useful for similar sites.
    MeSH term(s) Amphibians/physiology ; Animals ; Ecosystem ; Environmental Restoration and Remediation/methods ; Mining
    Language English
    Publishing date 2016-09
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1178791-0
    ISSN 1614-7499 ; 0944-1344
    ISSN (online) 1614-7499
    ISSN 0944-1344
    DOI 10.1007/s11356-015-5279-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Can we enhance amphibians’ habitat restoration in the post-mining areas?

    Klimaszewski, Krzysztof / Pacholik, Ewa / Snopek, Adam

    Environ Sci Pollut Res. 2016 Sept., v. 23, no. 17 p.16941-16945

    2016  

    Abstract: The study was aimed to evaluate the selected improvements of nature restoration in a depleted gravel pit. The study site consisted of four water reservoirs of different shapes and sizes, flooded after the gravel extraction ended. Ecological succession ... ...

    Abstract The study was aimed to evaluate the selected improvements of nature restoration in a depleted gravel pit. The study site consisted of four water reservoirs of different shapes and sizes, flooded after the gravel extraction ended. Ecological succession monitoring, conducted by the Warsaw University of Life Sciences students associated in the Student Scientific Association of Animal Sciences Faculty since the completion of mining, have focused on amphibians. A twofold approach upheld amphibian species population dynamics, as well as selected habitat elements. The restoration practices dedicated to habitat conditions enhancing have been proved to be definitely effective and useful for similar sites.
    Keywords amphibians ; ecological succession ; gravel ; gravel pits ; habitat conservation ; habitats ; population dynamics
    Language English
    Dates of publication 2016-09
    Size p. 16941-16945.
    Publishing place Springer Berlin Heidelberg
    Document type Article ; Online
    Note Resource is Open Access
    ZDB-ID 1178791-0
    ISSN 1614-7499 ; 0944-1344
    ISSN (online) 1614-7499
    ISSN 0944-1344
    DOI 10.1007/s11356-015-5279-8
    Database NAL-Catalogue (AGRICOLA)

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  5. Article: Efficiency determination of J-PET: first plastic scintillators-based PET scanner.

    Sharma, S / Baran, J / Chug, N / Curceanu, C / Czerwiński, E / Dadgar, M / Dulski, K / Eliyan, K / Gajos, A / Gupta-Sharma, N / Hiesmayr, B C / Kacprzak, K / Kapłon, Ł / Klimaszewski, K / Konieczka, P / Korcyl, G / Kozik, T / Krzemień, W / Kumar, D /
    Niedźwiecki, Sz / Panek, D / Parzych, S / Del Rio, E Perez / Raczyński, L / Choudhary, Shivani / Shopa, R Y / Skurzok, M / Stępień, E Ł / Tayefi, F / Tayefi, K / Wiślicki, W / Moskal, P

    EJNMMI physics

    2023  Volume 10, Issue 1, Page(s) 28

    Abstract: Background: The Jagiellonian Positron Emission Tomograph is the 3-layer prototype of the first scanner based on plastic scintillators, consisting of 192 half-metre-long strips with readouts at both ends. Compared to crystal-based detectors, plastic ... ...

    Abstract Background: The Jagiellonian Positron Emission Tomograph is the 3-layer prototype of the first scanner based on plastic scintillators, consisting of 192 half-metre-long strips with readouts at both ends. Compared to crystal-based detectors, plastic scintillators are several times cheaper and could be considered as a more economical alternative to crystal scintillators in future PETs. JPET is also a first multi-photon PET prototype. For the development of multi-photon detection, with photon characterized by the continuous energy spectrum, it is important to estimate the efficiency of J-PET as a function of energy deposition. The aim of this work is to determine the registration efficiency of the J-PET tomograph as a function of energy deposition by incident photons and the intrinsic efficiency of the J-PET scanner in detecting photons of different incident energies. In this study, 3-hit events are investigated, where 2-hits are caused by 511 keV photons emitted in [Formula: see text] annihilations, while the third hit is caused by one of the scattered photons. The scattered photon is used to accurately measure the scattering angle and thus the energy deposition. Two hits by a primary and a scattered photon are sufficient to calculate the scattering angle of a photon, while the third hit ensures the precise labeling of the 511 keV photons.
    Results: By comparing experimental and simulated energy distribution spectra, the registration efficiency of the J-PET scanner was determined in the energy deposition range of 70-270 keV, where it varies between 20 and 100[Formula: see text]. In addition, the intrinsic efficiency of the J-PET was also determined as a function of the energy of the incident photons.
    Conclusion: A method for determining registration efficiency as a function of energy deposition and intrinsic efficiency as a function of incident photon energy of the J-PET scanner was demonstrated. This study is crucial for evaluating the performance of the scanner based on plastic scintillators and its applications as a standard and multi-photon PET systems. The method may be also used in the calibration of Compton-cameras developed for the ion-beam therapy monitoring and simultaneous multi-radionuclide imaging in nuclear medicine.
    Language English
    Publishing date 2023-04-08
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2768912-8
    ISSN 2197-7364
    ISSN 2197-7364
    DOI 10.1186/s40658-023-00546-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Comparative studies of the sensitivities of sparse and full geometries of Total-Body PET scanners built from crystals and plastic scintillators.

    Dadgar, M / Parzych, S / Baran, J / Chug, N / Curceanu, C / Czerwiński, E / Dulski, K / Elyan, K / Gajos, A / Hiesmayr, B C / Kapłon, Ł / Klimaszewski, K / Konieczka, P / Korcyl, G / Kozik, T / Krzemien, W / Kumar, D / Niedzwiecki, S / Panek, D /
    Perez Del Rio, E / Raczyński, L / Sharma, S / Shivani, S / Shopa, R Y / Skurzok, M / Stepień, E Ł / Tayefi Ardebili, F / Tayefi Ardebili, K / Vandenberghe, S / Wiślicki, W / Moskal, P

    EJNMMI physics

    2023  Volume 10, Issue 1, Page(s) 62

    Abstract: 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 ... ...

    Abstract 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 configurations (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), different cross sections of plastic scintillator, and multiple numbers of plastic scintillator layers (2, 3, and 4), based on J-PET technology have been simulated by GATE software. Furthermore, Siemens' 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 1 mm 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 ([Formula: see text] 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 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.
    Language English
    Publishing date 2023-10-11
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2768912-8
    ISSN 2197-7364
    ISSN 2197-7364
    DOI 10.1186/s40658-023-00572-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Mites and internal parasites associated with the common dung beetle Geotrupes (Anoplotrupes) stercorosus (Hartmann in Scriba, 1791) in Poland.

    Sulgostowska, Teresa / Solarz, Krzysztof / Madej, Grażyna / Klimaszewski, Krzysztof

    Acta parasitologica

    2015  Volume 60, Issue 4, Page(s) 622–630

    Abstract: Common dung beetles collected in the "Sobieski Forest" (eastern border of Warsaw suburbs) were examined for the occurrence and prevalence of infections or infestations with intestinal parasites and phoretic mites in relation to soil characteristics and ... ...

    Abstract Common dung beetles collected in the "Sobieski Forest" (eastern border of Warsaw suburbs) were examined for the occurrence and prevalence of infections or infestations with intestinal parasites and phoretic mites in relation to soil characteristics and quality of the forest habitat. Endoparasitic fauna was represented by gregarines Didymophyes paradoxa, microsporidians Plistophora geotrupina and cysticerkoids of 2 tapeworms - Ditestolepis diaphana and Staphylocystis furcate. Prevalence of these infections was higher for beetles collected from rich habitats. Acarofauna was represented by hypopodes of Sancassania geotruporum (Astigmatina, Acaridae) and the following taxa of mesostigmatic mites: Alliphis halleri, Macrocheles glaber, Parasitus coleoptratorum and unidentified juvenile Laelapidae representative. Mites were most abundant in June, July and September. They were only slightly more numerously found on dung beetles from the rich habitats. Nonmetric multidimensional scaling, MDS (2D stress = 0.13) revealed significant similarities in the distribution of mite taxa between poor and rich sites and among the investigated months (June, July and September).
    MeSH term(s) Acari/classification ; Acari/growth & development ; Animals ; Apicomplexa/classification ; Apicomplexa/isolation & purification ; Cestoda/classification ; Cestoda/isolation & purification ; Coleoptera/parasitology ; Forests ; Intestines/parasitology ; Microsporidia/classification ; Microsporidia/isolation & purification ; Poland ; Prevalence ; Soil
    Chemical Substances Soil
    Language English
    Publishing date 2015-09-25
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1132735-2
    ISSN 1896-1851 ; 0065-1478 ; 1230-2821
    ISSN (online) 1896-1851
    ISSN 0065-1478 ; 1230-2821
    DOI 10.1515/ap-2015-0088
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Optimisation of the event-based TOF filtered back-projection for online imaging in total-body J-PET.

    Shopa, R Y / Klimaszewski, K / Kopka, P / Kowalski, P / Krzemień, W / Raczyński, L / Wiślicki, W / Chug, N / Curceanu, C / Czerwiński, E / Dadgar, M / Dulski, K / Gajos, A / Hiesmayr, B C / Kacprzak, K / Kapłon, Ł / Kisielewska, D / Korcyl, G / Krawczyk, N /
    Kubicz, E / Niedźwiecki, Sz / Raj, J / Sharma, S / Shivani / Stȩpień, E Ł / Tayefi, F / Moskal, P

    Medical image analysis

    2021  Volume 73, Page(s) 102199

    Abstract: We perform a parametric study of the newly developed time-of-flight (TOF) image reconstruction algorithm, proposed for the real-time imaging in total-body Jagiellonian PET (J-PET) scanners. The asymmetric 3D filtering kernel is applied at each most ... ...

    Abstract We perform a parametric study of the newly developed time-of-flight (TOF) image reconstruction algorithm, proposed for the real-time imaging in total-body Jagiellonian PET (J-PET) scanners. The asymmetric 3D filtering kernel is applied at each most likely position of electron-positron annihilation, estimated from the emissions of back-to-back γ-photons. The optimisation of its parameters is studied using Monte Carlo simulations of a 1-mm spherical source, NEMA IEC and XCAT phantoms inside the ideal J-PET scanner. The combination of high-pass filters which included the TOF filtered back-projection (FBP), resulted in spatial resolution, 1.5 times higher in the axial direction than for the conventional 3D FBP. For realistic 10-minute scans of NEMA IEC and XCAT, which require a trade-off between the noise and spatial resolution, the need for Gaussian TOF kernel components, coupled with median post-filtering, is demonstrated. The best sets of 3D filter parameters were obtained by the Nelder-Mead minimisation of the mean squared error between the resulting and reference images. The approach allows training the reconstruction algorithm for custom scans, using the IEC phantom, when the temporal resolution is below 50 ps. The image quality parameters, estimated for the best outcomes, were systematically better than for the non-TOF FBP.
    MeSH term(s) Algorithms ; Humans ; Image Processing, Computer-Assisted ; Monte Carlo Method ; Phantoms, Imaging ; Positron-Emission Tomography
    Language English
    Publishing date 2021-07-24
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1356436-5
    ISSN 1361-8423 ; 1361-8431 ; 1361-8415
    ISSN (online) 1361-8423 ; 1361-8431
    ISSN 1361-8415
    DOI 10.1016/j.media.2021.102199
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Book ; Online: J-PET detection modules based on plastic scintillators for performing studies with positron and positronium beams

    Sharma, S. / Baran, J. / Brusa, R. S. / Caravita, R. / Chug, N. / Coussat, A. / Curceanu, C. / Czerwinski, E. / Dadgar, M. / Dulski, K. / Eliyan, K. / Gajos, A. / Hiesmayr, B. C. / Kacprzak, K. / Kaplon, L. / Klimaszewski, K. / Konieczka, P. / Korcyl, G. / Kozik, T. /
    Krzemien, W. / Kumar, D. / Mariazzi, S. / Niedzwiecki, S. / Panasa, L. / Parzych, S. / Povolo, L. / del Rio, E. Perez / Raczynski, L. / Shivani / Shopa, R. Y. / Skurzok, M. / Stepien, E. L. / Tayefi, F. / Tayefi, K. / Wislicki, W. / Moskal, P.

    2023  

    Abstract: The J-PET detector, which consists of inexpensive plastic scintillators, has demonstrated its potential in the study of fundamental physics. In recent years, a prototype with 192 plastic scintillators arranged in 3 layers has been optimized for the study ...

    Abstract The J-PET detector, which consists of inexpensive plastic scintillators, has demonstrated its potential in the study of fundamental physics. In recent years, a prototype with 192 plastic scintillators arranged in 3 layers has been optimized for the study of positronium decays. This allows performing precision tests of discrete symmetries (C, P, T) in the decays of positronium atoms. Moreover, thanks to the possibility of measuring the polarization direction of the photon based on Compton scattering, the predicted entanglement between the linear polarization of annihilation photons in positronium decays can also be studied. Recently, a new J-PET prototype was commissioned, based on a modular design of detection units. Each module consists of 13 plastic scintillators and can be used as a stand-alone, compact and portable detection unit. In this paper, the main features of the J-PET detector, the modular prototype and their applications for possible studies with positron and positronium beams are discussed. Preliminary results of the first test experiment performed on two detection units in the continuous positron beam recently developed at the Antimatter Laboratory (AML) of Trento are also reported.
    Keywords Physics - Instrumentation and Detectors
    Subject code 621
    Publishing date 2023-01-07
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Testing CPT symmetry in ortho-positronium decays with positronium annihilation tomography.

    Moskal, P / Gajos, A / Mohammed, M / Chhokar, J / Chug, N / Curceanu, C / Czerwiński, E / Dadgar, M / Dulski, K / Gorgol, M / Goworek, J / Hiesmayr, B C / Jasińska, B / Kacprzak, K / Kapłon, Ł / Karimi, H / Kisielewska, D / Klimaszewski, K / Korcyl, G /
    Kowalski, P / Krawczyk, N / Krzemień, W / Kozik, T / Kubicz, E / Niedźwiecki, S / Parzych, S / Pawlik-Niedźwiecka, M / Raczyński, L / Raj, J / Sharma, S / Choudhary, S / Shopa, R Y / Sienkiewicz, A / Silarski, M / Skurzok, M / Stępień, E Ł / Tayefi, F / Wiślicki, W

    Nature communications

    2021  Volume 12, Issue 1, Page(s) 5658

    Abstract: Charged lepton system symmetry under combined charge, parity, and time-reversal transformation (CPT) remains scarcely tested. Despite stringent quantum-electrodynamic limits, discrepancies in predictions for the electron-positron bound state (positronium ...

    Abstract Charged lepton system symmetry under combined charge, parity, and time-reversal transformation (CPT) remains scarcely tested. Despite stringent quantum-electrodynamic limits, discrepancies in predictions for the electron-positron bound state (positronium atom) motivate further investigation, including fundamental symmetry tests. While CPT noninvariance effects could be manifested in non-vanishing angular correlations between final-state photons and spin of annihilating positronium, measurements were previously limited by knowledge of the latter. Here, we demonstrate tomographic reconstruction techniques applied to three-photon annihilations of ortho-positronium atoms to estimate their spin polarisation without magnetic field or polarised positronium source. We use a plastic-scintillator-based positron-emission-tomography scanner to record ortho-positronium (o-Ps) annihilations with single-event estimation of o-Ps spin and determine the complete spectrum of an angular correlation operator sensitive to CPT-violating effects. We find no violation at the precision level of 10
    Language English
    Publishing date 2021-09-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-021-25905-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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