Towards Real-time Remote Processing of Laparoscopic Video

Laparoscopic surgery is a minimally invasive technique where surgeons insert a small video camera into the patient\u27s body to visualize internal organs and use small tools to perform these procedures. However, the benefit of small incisions has a disadvantage of limited visualization of subsurface tissues. Image-guided surgery (IGS) uses pre-operative and intra-operative images to map subsurface structures and can reduce the limitations of laparoscopic surgery. One particular laparoscopic system is the daVinci-si robotic surgical vision system. The video streams generate approximately 360 megabytes of data per second, demonstrating a trend toward increased data sizes in medicine, primarily due to higher-resolution video cameras and imaging equipment. Real-time processing this large stream of data on a bedside PC, single or dual node setup, may be challenging and a high-performance computing (HPC) environment is not typically available at the point of care. To process this data on remote HPC clusters at the typical 30 frames per second rate (fps), it is required that each 11.9 MB (1080p) video frame be processed by a server and returned within the time this frame is displayed or 1/30th of a second. The ability to acquire, process, and visualize data in real time is essential for the performance of complex tasks as well as minimizing risk to the patient. We have implemented and compared performance of compression, segmentation and registration algorithms on Clemson\u27s Palmetto supercomputer using dual Nvidia graphics processing units (GPUs) per node and compute unified device architecture (CUDA) programming model. We developed three separate applications that run simultaneously: video acquisition, image processing, and video display. The image processing application allows several algorithms to run simultaneously on different cluster nodes and transfer images through message passing interface (MPI). Our segmentation and registration algorithms resulted in an acceleration factor of around 2 and 8 times respectively. To achieve a higher frame rate, we also resized images and reduced the overall processing time. As a result, using high-speed network to access computing clusters with GPUs to implement these algorithms in parallel will improve surgical procedures by providing real-time medical image processing and laparoscopic data

Fast algorithm for real-time rings reconstruction

The GAP project is dedicated to study the application of GPU in several contexts in which real-time response is important to take decisions. The definition of real-time depends on the application under study, ranging from answer time of μs up to several hours in case of very computing intensive task. During this conference we presented our work in low level triggers [1] [2] and high level triggers [3] in high energy physics experiments, and specific application for nuclear magnetic resonance (NMR) [4] [5] and cone-beam CT [6]. Apart from the study of dedicated solution to decrease the latency due to data transport and preparation, the computing algorithms play an essential role in any GPU application. In this contribution, we show an original algorithm developed for triggers application, to accelerate the ring reconstruction in RICH detector when it is not possible to have seeds for reconstruction from external trackers

Brain-Inspired Computing

This open access book constitutes revised selected papers from the 4th International Workshop on Brain-Inspired Computing, BrainComp 2019, held in Cetraro, Italy, in July 2019. The 11 papers presented in this volume were carefully reviewed and selected for inclusion in this book. They deal with research on brain atlasing, multi-scale models and simulation, HPC and data infra-structures for neuroscience as well as artificial and natural neural architectures

Charting NeuLAND: Towards multi-neutron reconstruction with the New Large Area Neutron Detector and The virtual γ-ray spectrometer G4Horus

This thesis presents work on the New Large Area Neutron Detector NeuLAND, which will be used at the upcoming Facility for Antiproton and Ion Research (FAIR), Germany. Assembly steps for detector modules are described, followed by experiments performed with the NeuLAND Demonstrator in Japan. The detector is also assembled virtually for Monte Carlo simulations, including a conversion process from energy depositions to experimental look-alike events. This detector response is in good agreement with experimental data from Japan. Performance and behavior of newly developed reconstruction methods are mapped out for different detector sizes. These algorithms can reconstruct multiplicity and primary interaction points for many incoming neutrons. In addition, the groundwork for event reconstruction with neural networks is laid. In the second part, the Geant4 application G4Horus is presented, which implements a virtual version of the HORUS γ-ray spectrometer used at the Institute for Nuclear Physics, University of Cologne. The high purity germanium (HPGe) detectors in this spectrometer are often used to measure γ-rays from 5 MeV to 10 MeV. No standardized calibration sources are available at these energies, and the efficiency calibration is challenging. G4Horus alleviates this problem with easy to use efficiency simulations. More complex experiments with particle detectors and respective data analysis procedures can be understood and improved with matching simulations. Here, G4Horus provides listmode data with simulated particle-γ coincidences

EDEN: A high-performance, general-purpose, NeuroML-based neural simulator

Modern neuroscience employs in silico experimentation on ever-increasing and more detailed neural networks. The high modelling detail goes hand in hand with the need for high model reproducibility, reusability and transparency. Besides, the size of the models and the long timescales under study mandate the use of a simulation system with high computational performance, so as to provide an acceptable time to result. In this work, we present EDEN (Extensible Dynamics Engine for Networks), a new general-purpose, NeuroML-based neural simulator that achieves both high model flexibility and high computational performance, through an innovative model-analysis and code-generation technique. The simulator runs NeuroML v2 models directly, eliminating the need for users to learn yet another simulator-specific, model-specification language. EDEN's functional correctness and computational performance were assessed through NeuroML models available on the NeuroML-DB and Open Source Brain model repositories. In qualitative experiments, the results produced by EDEN were verified against the established NEURON simulator, for a wide range of models. At the same time, computational-performance benchmarks reveal that EDEN runs up to 2 orders-of-magnitude faster than NEURON on a typical desktop computer, and does so without additional effort from the user. Finally, and without added user effort, EDEN has been built from scratch to scale seamlessly over multiple CPUs and across computer clusters, when available.Comment: 29 pages, 9 figure

Tractografia em tempo real através de unidades de processamento gráfico

Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro Tecnológico, Programa de Pós-Graduação em Ciência da Computação, Florianópolis, 2009.A tractografia por propagação de linhas é um método que, com base na ressonância magnética de tensores de difusão (DT-MRI), revela in vivo a disposição dos tratos neurais no cérebro humano. O alto custo computacional da tractografia, porém, implica um tempo de espera significativamente longo para o cálculo e exibição dos resultados. Esse tempo pode ser reduzido executando-se a tractografia de forma paralela, já que as trajetórias encontradas pelo método de propagação de linhas são independentes umas das outras. Uma plataforma atrativa para a execução paralela de programas é oferecida pelas unidades de processamento gráfico (GPUs) das placas de vídeo atuais. Desse modo, este trabalho propõe a execução paralela da tractografia por propagação de linhas em GPUs através da tecnologia CUDA. Experimentos foram conduzidos para avaliar o desempenho da tractografia em um processador central (CPU) e quatro GPUs distintas. Os resultados mostram que as GPUs são, no melhor caso, até 38 vezes mais velozes que a CPU na execução da tractografia, e até 8 vezes mais rápidas no pior caso. A velocidade obtida através das GPUs permite que os resultados tractográficos sejam calculados e exibidos em tempo real para um número de trajetórias superior a 3.000

Ono: an open platform for social robotics

In recent times, the focal point of research in robotics has shifted from industrial ro- bots toward robots that interact with humans in an intuitive and safe manner. This evolution has resulted in the subfield of social robotics, which pertains to robots that function in a human environment and that can communicate with humans in an int- uitive way, e.g. with facial expressions. Social robots have the potential to impact many different aspects of our lives, but one particularly promising application is the use of robots in therapy, such as the treatment of children with autism. Unfortunately, many of the existing social robots are neither suited for practical use in therapy nor for large scale studies, mainly because they are expensive, one-of-a-kind robots that are hard to modify to suit a specific need. We created Ono, a social robotics platform, to tackle these issues. Ono is composed entirely from off-the-shelf components and cheap materials, and can be built at a local FabLab at the fraction of the cost of other robots. Ono is also entirely open source and the modular design further encourages modification and reuse of parts of the platform

Heterogeneous computing systems for vision-based multi-robot tracking

Irwansyah A. Heterogeneous computing systems for vision-based multi-robot tracking. Bielefeld: Universität Bielefeld; 2017

Exploiting All-Programmable System on Chips for Closed-Loop Real-Time Neural Interfaces

High-density microelectrode arrays (HDMEAs) feature thousands of recording electrodes in a single chip with an area of few square millimeters. The obtained electrode density is comparable and even higher than the typical density of neuronal cells in cortical cultures. Commercially available HDMEA-based acquisition systems are able to record the neural activity from the whole array at the same time with submillisecond resolution. These devices are a very promising tool and are increasingly used in neuroscience to tackle fundamental questions regarding the complex dynamics of neural networks. Even if electrical or optical stimulation is generally an available feature of such systems, they lack the capability of creating a closed-loop between the biological neural activity and the artificial system. Stimuli are usually sent in an open-loop manner, thus violating the inherent working basis of neural circuits that in nature are constantly reacting to the external environment. This forbids to unravel the real mechanisms behind the behavior of neural networks. The primary objective of this PhD work is to overcome such limitation by creating a fullyreconfigurable processing system capable of providing real-time feedback to the ongoing neural activity recorded with HDMEA platforms. The potentiality of modern heterogeneous FPGAs has been exploited to realize the system. In particular, the Xilinx Zynq All Programmable System on Chip (APSoC) has been used. The device features reconfigurable logic, specialized hardwired blocks, and a dual-core ARM-based processor; the synergy of these components allows to achieve high elaboration performances while maintaining a high level of flexibility and adaptivity. The developed system has been embedded in an acquisition and stimulation setup featuring the following platforms: \u2022 3\ub7Brain BioCam X, a state-of-the-art HDMEA-based acquisition platform capable of recording in parallel from 4096 electrodes at 18 kHz per electrode. \u2022 PlexStim\u2122 Electrical Stimulator System, able to generate electrical stimuli with custom waveforms to 16 different output channels. \u2022 Texas Instruments DLP\uae LightCrafter\u2122 Evaluation Module, capable of projecting 608x684 pixels images with a refresh rate of 60 Hz; it holds the function of optical stimulation. All the features of the system, such as band-pass filtering and spike detection of all the recorded channels, have been validated by means of ex vivo experiments. Very low-latency has been achieved while processing the whole input data stream in real-time. In the case of electrical stimulation the total latency is below 2 ms; when optical stimuli are needed, instead, the total latency is a little higher, being 21 ms in the worst case. The final setup is ready to be used to infer cellular properties by means of closed-loop experiments. As a proof of this concept, it has been successfully used for the clustering and classification of retinal ganglion cells (RGCs) in mice retina. For this experiment, the light-evoked spikes from thousands of RGCs have been correctly recorded and analyzed in real-time. Around 90% of the total clusters have been classified as ON- or OFF-type cells. In addition to the closed-loop system, a denoising prototype has been developed. The main idea is to exploit oversampling techniques to reduce the thermal noise recorded by HDMEAbased acquisition systems. The prototype is capable of processing in real-time all the input signals from the BioCam X, and it is currently being tested to evaluate the performance in terms of signal-to-noise-ratio improvement