VIOLA - A multi-purpose and web-based visualization tool for neuronal-network simulation output

Neuronal network models and corresponding computer simulations are invaluable tools to aid the interpretation of the relationship between neuron properties, connectivity and measured activity in cortical tissue. Spatiotemporal patterns of activity propagating across the cortical surface as observed experimentally can for example be described by neuronal network models with layered geometry and distance-dependent connectivity. The interpretation of the resulting stream of multi-modal and multi-dimensional simulation data calls for integrating interactive visualization steps into existing simulation-analysis workflows. Here, we present a set of interactive visualization concepts called views for the visual analysis of activity data in topological network models, and a corresponding reference implementation VIOLA (VIsualization Of Layer Activity). The software is a lightweight, open-source, web-based and platform-independent application combining and adapting modern interactive visualization paradigms, such as coordinated multiple views, for massively parallel neurophysiological data. For a use-case demonstration we consider spiking activity data of a two-population, layered point-neuron network model subject to a spatially confined excitation originating from an external population. With the multiple coordinated views, an explorative and qualitative assessment of the spatiotemporal features of neuronal activity can be performed upfront of a detailed quantitative data analysis of specific aspects of the data. Furthermore, ongoing efforts including the European Human Brain Project aim at providing online user portals for integrated model development, simulation, analysis and provenance tracking, wherein interactive visual analysis tools are one component. Browser-compatible, web-technology based solutions are therefore required. Within this scope, with VIOLA we provide a first prototype.Comment: 38 pages, 10 figures, 3 table

PlantES: A plant electrophysiological multi-source data online analysis and sharing platform

At present, plant electrophysiological data volumes and complexity are increasing rapidly. It causes the demand for efficient management of big data, data sharing among research groups, and fast analysis. In this paper, we proposed PlantES (Plant Electrophysiological Data Sharing), a distributed computing-based prototype system that can be used to store, manage, visualize, analyze, and share plant electrophysiological data. We deliberately designed a storage schema to manage the multi-source plant electrophysiological data by integrating distributed storage systems HDFS and HBase to access all kinds of files efficiently. To improve the online analysis efficiency, parallel computing algorithms on Spark were proposed and implemented, e.g., plant electrical signals extraction method, the adaptive derivative threshold algorithm, and template matching algorithm. The experimental results indicated that Spark efficiently improves the online analysis. Meanwhile, the online visualization and sharing of multiple types of data in the web browser were implemented. Our prototype platform provides a solution for web-based sharing and analysis of plant electrophysiological multi-source data and improves the comprehension of plant electrical signals from a systemic perspective

MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data

Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that include some aspect of 3-D visualization, including both free and commercial products. These applications range from highly specific programs for a single modality, to general purpose toolkits that include many image processing functions in addition to visualization. However, few if any of these combine both stand-alone and remote multi-modality visualization in an open source, portable and extensible tool that is easy to install and use, yet can be included as a component of a larger information system. We have developed a new open source multimodality 3-D visualization application, called MindSeer, that has these features: integrated and interactive 3-D volume and surface visualization, Java and Java3D for true cross-platform portability, one-click installation and startup, integrated data management to help organize large studies, extensibility through plugins, transparent remote visualization, and the ability to be integrated into larger information management systems. We describe the design and implementation of the system, as well as several case studies that demonstrate its utility. These case studies are available as tutorials or demos on the associated website: http://sig.biostr.washington.edu/projects/MindSeer MindSeer provides a powerful visualization tool for multimodality neuroimaging data. Its architecture and unique features also allow it to be extended into other visualization domains within biomedicine

Emotions and cognitive workload in economic decision processes - A NeuroIS Approach

The influence of cognitive and emotions on decision processes have been recently highlighted. Emotions interplay with the process of cognition, and determine decision processes. In this work, the role of external and internal influences on economic decision processes are studied. A NeuroIS method is applied for measuring emotions and cognitive workload. The lack of a suitable experimental platform for performing NeuroIS studies was recognized and the platform Brownie was developed and evaluated

A Neuroimaging Web Interface for Data Acquisition, Processing and Visualization of Multimodal Brain Images

Structural and functional brain images are generated as essential modalities for medical experts to learn about the different functions of the brain. These images are typically visually inspected by experts. Many software packages are available to process medical images, but they are complex and difficult to use. The software packages are also hardware intensive. As a consequence, this dissertation proposes a novel Neuroimaging Web Services Interface (NWSI) as a series of processing pipelines for a common platform to store, process, visualize and share data. The NWSI system is made up of password-protected interconnected servers accessible through a web interface. The web-interface driving the NWSI is based on Drupal, a popular open source content management system. Drupal provides a user-based platform, in which the core code for the security and design tools are updated and patched frequently. New features can be added via modules, while maintaining the core software secure and intact. The webserver architecture allows for the visualization of results and the downloading of tabulated data. Several forms are ix available to capture clinical data. The processing pipeline starts with a FreeSurfer (FS) reconstruction of T1-weighted MRI images. Subsequently, PET, DTI, and fMRI images can be uploaded. The Webserver captures uploaded images and performs essential functionalities, while processing occurs in supporting servers. The computational platform is responsive and scalable. The current pipeline for PET processing calculates all regional Standardized Uptake Value ratios (SUVRs). The FS and SUVR calculations have been validated using Alzheimer\u27s Disease Neuroimaging Initiative (ADNI) results posted at Laboratory of Neuro Imaging (LONI). The NWSI system provides access to a calibration process through the centiloid scale, consolidating Florbetapir and Florbetaben tracers in amyloid PET images. The interface also offers onsite access to machine learning algorithms, and introduces new heat maps that augment expert visual rating of PET images. NWSI has been piloted using data and expertise from Mount Sinai Medical Center, the 1Florida Alzheimer’s Disease Research Center (ADRC), Baptist Health South Florida, Nicklaus Children\u27s Hospital, and the University of Miami. All results were obtained using our processing servers in order to maintain data validity, consistency, and minimal processing bias

Efficiency evaluation of external environments control using bio-signals

There are many types of bio-signals with various control application prospects. This dissertation regards possible application domain of electroencephalographic signal. The implementation of EEG signals, as a source of information used for control of external devices, became recently a growing concern in the scientific world. Application of electroencephalographic signals in Brain-Computer Interfaces (BCI) (variant of Human-Computer Interfaces (HCI)) as an implement, which enables direct and fast communication between the human brain and an external device, has become recently very popular. Currently available on the market, BCI solutions require complex signal processing methodology, which results in the need of an expensive equipment with high computing power. In this work, a study on using various types of EEG equipment in order to apply the most appropriate one was conducted. The analysis of EEG signals is very complex due to the presence of various internal and external artifacts. The signals are also sensitive to disturbances and non-stochastic, what makes the analysis a complicated task. The research was performed on customised (built by the author of this dissertation) equipment, on professional medical device and on Emotiv EPOC headset. This work concentrated on application of an inexpensive, easy to use, Emotiv EPOC headset as a tool for gaining EEG signals. The project also involved application of embedded system platform - TS-7260. That solution caused limits in choosing an appropriate signal processing method, as embedded platforms characterise with a little efficiency and low computing power. That aspect was the most challenging part of the whole work. Implementation of the embedded platform enables to extend the possible future application of the proposed BCI. It also gives more flexibility, as the platform is able to simulate various environments. The study did not involve the use of traditional statistical or complex signal processing methods. The novelty of the solution relied on implementation of the basic mathematical operations. The efficiency of this method was also presented in this dissertation. Another important aspect of the conducted study is that the research was carried out not only in a laboratory, but also in an environment reflecting real-life conditions. The results proved efficiency and suitability of the implementation of the proposed solution in real-life environments. The further study will focus on improvement of the signal-processing method and application of other bio-signals - in order to extend the possible applicability and ameliorate its effectiveness

Autonomous open-source electric wheelchair platform with internet-of-things and proportional-integral-derivative control

This study aims to improve the working model of autonomous wheelchair navigation for disabled patients using the internet of things (IoT). A proportional-integral-derivative (PID) control algorithm is applied to the autonomous wheelchair to control movement based on position coordinates and orientation provided by the global positioning system (GPS) and digital compass sensor. This system is controlled through the IoT system, which can be operated from a web browser. Autonomous wheelchairs are handled using a waypoint algorithm; ESP8266 is used as a microcontroller unit that acts as a bridge for transmitting data obtained by sensors and controlling the direct current (DC) motors as actuators. The proposed system and the autonomous wheelchair performance gave satisfactory results with a longitude and latitude error of 1.1 meters to 4.5 meters. This error is obtained because of the limitations of GPS with the type of Ublox Neo-M8N. As a starting point for further research, a mathematical model of a wheelchair was created, and pure pursuit control algorithm was used to simulate the movement. An open-source autonomous IoT platform for electric wheelchairs has been successfully created; this platform can help nurses and caretakers