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

Evaluation of Single-Chip, Real-Time Tomographic Data Processing on FPGA - SoC Devices

A novel approach to tomographic data processing has been developed and evaluated using the Jagiellonian PET (J-PET) scanner as an example. We propose a system in which there is no need for powerful, local to the scanner processing facility, capable to reconstruct images on the fly. Instead we introduce a Field Programmable Gate Array (FPGA) System-on-Chip (SoC) platform connected directly to data streams coming from the scanner, which can perform event building, filtering, coincidence search and Region-Of-Response (ROR) reconstruction by the programmable logic and visualization by the integrated processors. The platform significantly reduces data volume converting raw data to a list-mode representation, while generating visualization on the fly.Comment: IEEE Transactions on Medical Imaging, 17 May 201

Performance Modeling of Parallel Applications on MPSoCs

In this paper we present a new technique for automatically measuring the performance of tasks, functions or arbitrary parts of a program on a multiprocessor embedded system. The technique instruments the tasks described by OpenMP, used to represent the task parallelism, while ad hoc pragmas in the source indicate other pieces of code to profile. The annotations and the instrumentation are completely target-independent, so the same code can be measured on different target architectures, on simulators or on prototypes. We validate the approach on a single and on a dual LEON 3 platform synthesized on FPGA, demonstrating a low instrumentation overhead. We show how the information obtained with this technique can be easily exploited in a hardware/software design space exploration tool, by estimating, with good accuracy, the speed-up of a parallel application given the profiling on the single processor prototype

Computing support for advanced medical data analysis and imaging

We discuss computing issues for data analysis and image reconstruction of PET-TOF medical scanner or other medical scanning devices producing large volumes of data. Service architecture based on the grid and cloud concepts for distributed processing is proposed and critically discussed.Comment: 9 p, 3 figs, based on talk given at Symposium on Positron Emission Tomography, Sept. 19-22, 2013, Jagiellonian University, Krak\'ow, P

Sistemas de tomografia por emissão de positrões para pequenos animais

The growing demand for PET scanners in preclinical studies combined with the high cost of those equipments increased the interest in the development of new high performance and low cost system, made possible due to the recent technological developments in the industry of radiation detection. Is this work, we present two low cost PET scanners. The first is the DRIM-PET, a PET scanner with improved spatial resolution through the determination of the depth-of-interaction of the photons in the detectors, correcting the parallax effect. The use of MPPCs and wavelength-shifting fibers for light detection allows to reduce the number of components, reducing the device cost. We present the performance characterization of an unitary cell of the DRIM-PET system, as a proof-of-concept, and we report a depth-of-interaction resolution of the order of 7mm. The other PET scanner presented is the EasyPET 3D, with capabilities of acquire volumetric images and execute spectroscopy. The use of a rotation system for the detecting cells allows to reduce the number of cells thus reducing the cost of the device, keeping high spatial resolution bellow 1.5mm, uniform along the FOV, which is variable up to 60mm. Image quality was evaluated using the NEMA NU-2008 standard, the commercial prototype for the first time shown and the first preclinical acquisitions are shown for 18F-FDG and 18F-NaF, for mouse brain and skeleton imaging, respectively. Finally, the development of a simulation toolkit written in GATE for the EasyPET prototype (2D), commercialized by the Italian company CAEN, SpA, allows students to perform simple tasks the simulate experimental procedures such as the evaluation of the effect of different coincidence time and energy windows for the reconstructed image, for radioactive sources at different locations within the FOV. The platform can be included in the official code EduGATE as a supplementary module.A crescente procura por tomógrafos PET para estudos pré-clínicos aliada ao elevado custo destes equipamentos, fez aumentar o interesse no desenvolvimento de novos sistemas de elevada performance a baixo custo, possibilitados pelos novos desenvolvimentos tecnológicos na industria de deteção de radiação. Dois sistemas de baixo custo são apresentados no âmbito deste trabalho. O primeiro é o DRIM-PET, um tomógrafo PET com melhorada resolução espacial através da determinação do ponto de interação da radiação nos detetores. A correção do efeito de paralaxe é feita usando MPPCs e fibras conversoras de luz para deteção da luz, mantendo um reduzido número de detetores. É apresentada a caracterização experimental de uma célula unitária do DRIM-PET como prova de conceito, onde a resolução espacial na determinação do ponto de interação obtida é da ordem de 7mm. O outro tomógrafo PET apresentado é o EasyPET 3D, com capacidade de aquisição de imagens em 3D e espectroscopia de raios. O uso de um sistema de rotação das células detectoras para aquisição de imagens permite reduzir o número de células, mantendo elevada resolução em posição, da ordem de 1.5mm, para um campo de visão variável até 60mm, reduzindo o custo do equipamento. A qualidade de imagem do dispositivo foi avaliada usando a norma NEMA NU-2008, o protótipo comercial apresentado e as primeiras aquisições pré-clínicas com 18F-FDG e 18F-NaF apresentadas, em imagens do cérebro e do esqueleto em ratos, respetivamente. Finalmente, o desenvolvimento de uma plataforma de simulação para o primeiro sistema EasyPET (2D), comercializado pela empresa CAEN, SpA, permite que estudantes executem tarefas simples que simulam as aquisições experimentais, como o efeito de diferentes janelas de tempo e energia para a imagem reconstruida, para fontes radioativas colocadas em diferentes localizações no FOV. A plataforma pode ser incluída no pacote EduGATE como um módulo suplementar.P. M. M. Correia is supported by the FCT (Lisbon) scholarship BD/52330/2013 under the PhD FCT program DAEPHYS, and is grateful to the I3N laboratory, funded by UID/CTM/50025/2013. This work was partially supported by project POCI-01-0145-FEDER-016855 and PTDC/BBB-IMG/4909/2014, and project easyPET nº 17823, through COMPETE, FEDER, POCI and FCT (Lisbon) programs.Programa Doutoral em Engenharia Civi

Advanced photonic and electronic systems WILGA 2018

WILGA annual symposium on advanced photonic and electronic systems has been organized by young scientist for young scientists since two decades. It traditionally gathers around 400 young researchers and their tutors. Ph.D students and graduates present their recent achievements during well attended oral sessions. Wilga is a very good digest of Ph.D. works carried out at technical universities in electronics and photonics, as well as information sciences throughout Poland and some neighboring countries. Publishing patronage over Wilga keep Elektronika technical journal by SEP, IJET and Proceedings of SPIE. The latter world editorial series publishes annually more than 200 papers from Wilga. Wilga 2018 was the XLII edition of this meeting. The following topical tracks were distinguished: photonics, electronics, information technologies and system research. The article is a digest of some chosen works presented during Wilga 2018 symposium. WILGA 2017 works were published in Proc. SPIE vol.10445. WILGA 2018 works were published in Proc. SPIE vol.10808

PhysioSkin: Rapid Fabrication of Skin-Conformal Physiological Interfaces

Advances in rapid prototyping platforms have made physiological sensing accessible to a wide audience. However, off-the-shelf electrodes commonly used for capturing biosignals are typically thick, non-conformal and do not support customization. We present PhysioSkin, a rapid, do-it-yourself prototyping method for fabricating custom multi-modal physiological sensors, using commercial materials and a commodity desktop inkjet printer. It realizes ultrathin skin-conformal patches (~1μm) and interactive textiles that capture sEMG, EDA and ECG signals. It further supports fabricating devices with custom levels of thickness and stretchability. We present detailed fabrication explorations on multiple substrate materials, functional inks and skin adhesive materials. Informed from the literature, we also provide design recommendations for each of the modalities. Evaluation results show that the sensor patches achieve a high signal-to-noise ratio. Example applications demonstrate the functionality and versatility of our approach for prototyping a next generation of physiological devices that intimately couple with the human body

Chapter 5: Evaluation

The OTiS (Online Teaching in Scotland) programme, run by the now defunct Scotcit programme, ran an International e-Workshop on Developing Online Tutoring Skills which was held between 8–12 May 2000. It was organised by Heriot–Watt University, Edinburgh and The Robert Gordon University, Aberdeen, UK. Out of this workshop came the seminal Online Tutoring E-Book, a generic primer on e-learning pedagogy and methodology, full of practical implementation guidelines. Although the Scotcit programme ended some years ago, the E-Book has been copied to the SONET site as a series of PDF files, which are now available via the ALT Open Access Repository. The editor, Carol Higgison, is currently working in e-learning at the University of Bradford (see her staff profile) and is the Chair of the Association for Learning Technology (ALT)

Embedded machine learning using microcontrollers in wearable and ambulatory systems for health and care applications: a review

The use of machine learning in medical and assistive applications is receiving significant attention thanks to the unique potential it offers to solve complex healthcare problems for which no other solutions had been found. Particularly promising in this field is the combination of machine learning with novel wearable devices. Machine learning models, however, suffer from being computationally demanding, which typically has resulted on the acquired data having to be transmitted to remote cloud servers for inference. This is not ideal from the system’s requirements point of view. Recently, efforts to replace the cloud servers with an alternative inference device closer to the sensing platform, has given rise to a new area of research Tiny Machine Learning (TinyML). In this work, we investigate the different challenges and specifications trade-offs associated to existing hardware options, as well as recently developed software tools, when trying to use microcontroller units (MCUs) as inference devices for health and care applications. The paper also reviews existing wearable systems incorporating MCUs for monitoring, and management, in the context of different health and care intended uses. Overall, this work addresses the gap in literature targeting the use of MCUs as edge inference devices for healthcare wearables. Thus, can be used as a kick-start for embedding machine learning models on MCUs, focusing on healthcare wearables