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Multi-scale brain simulation with TVB-NEST

This Python package offers a convenient interface to set-up co-simulation models that simulate TVB large-scale brain network models that interact with NEST spiking neuron models. NEST simulates neural activity at the microscopic spatial scale of single neurons or neuron networks. On the other hand, The Virtual brain simulates at the mesoscopic or macroscopic scales of large neural populations or brain regions. Here, both are brought together to enable neuroscientists to study how these different scales interact and how different scales inform activity "from the bottom up" and "down from the top". A generic Python interface allows users to quickly and conveniently set up a parallel simulation in TVB and in NEST and automatically handles the exchange of currents, spikes, voltages, etc. between the different scales. Although the technical aspect of this tool is realized, the scientific part is a work in progress and we are continuously enriching the coupling between scales such that biophysical plausibility is maintained. The TVB+NEST bundle software package -- available as an easy-to-use Docker image container -- combines the sophistication and flexibility of NEST's spiking neuron simulation infrastructure with TVB's whole-brain simulation, processing, analyses and visualisation capabilities.

Whole-brain simulationModelling and simulation

openMINDS metadata for TVB-ready data

This Jupyter notebook contains Python code for creating openMINDS JSON-LD metadata collections for TVB-ready data. The code in this notebook was used to generate openMINDS metadata for curation of TVB-on-EBRAINS datasets using openMINDS v1. An overview over TVB-on-EBRAINS services is provided in the preprint The openMINDS schema standard specification is hosted in the repository

Whole-brain simulationModelling and simulation

The Virtual Brain

The Virtual Brain (TVB) is an open-source platform for constructing and simulating personalised brain network models. The TVB-on-EBRAINS ecosystem includes a variety of prepackaged modules, integrated simulation tools, pipelines and data sets for easy and immediate use on EBRAINS. Process your large cohort databases and use these results to develop potential medical treatments, therapies or diagnostic procedures.

Modelling and simulationWhole-brain simulation

The Virtual Brain Web-App

Access the TVB GUI from the Internet and simulate brain network models on HCP. TheVirtualBrain is a framework for the simulation of the dynamics of large-scale brain networks with biologically realistic connectivity. TheVirtualBrain uses tractographic data (DTI/DSI) to generate connectivity matrices and build cortical and subcortical brain networks. The connectivity matrix defines the connection strengths and time delays via signal transmission between all network nodes. Various neural mass models are available in the repertoire of TheVirtualBrain and define the dynamics of a network node. Together, the neural mass models at the network nodes and the connectivity matrix define the Virtual Brain. TheVirtualBrain simulates and generates the time courses of various forms of neural activity including Local Field Potentials (LFP) and firing rate, as well as brain imaging data such as EEG, MEG and BOLD activations as observed in fMRI. TheVirtualBrain is foremost a scientific simulation platform and provides all means necessary to generate, manipulate and visualize connectivity and network dynamics. In addition, TheVirtualBrain comprises a set of classical time series analysis tools, structural and functional connectivity analysis tools, as well as parameter exploration facilities. An overview over TVB-on-EBRAINS services is provided in the preprint

Modelling and simulationWhole-brain simulation

TVB Brain Atlas Viewer

A viewer that allows users to view brain atlasses on top of a 3d brain model. The Brain Atlas Viewer allows users to inspect the location and shape of different brain regions and their associated function. Brain regions can be selected by anatomy or by function. Descriptions are available in English, Arabic, Hebrew, and German. Regions are annotated with their function. TVB Brain Atlas Viewer is an interactive software that can be operated via touch screen. It was part of the HBP Travelling Exhibition that started in July 2019 at Bloomfield Museum in Jerusalem organized by the HBP Museum Program (SP11). An overview over TVB-on-EBRAINS services is provided in the preprint

Whole-brain simulationModelling and simulationBrain atlases


TVB-HPC provides a framework for generating high-performance computational kernels which can be run on HPC systems with or without hardware accelerators for large scale parameter fitting of brain models An overview over TVB-on-EBRAINS services is provided in the preprint

Whole-brain simulationModelling and simulation

TVB image processing pipeline

The TVB pipeline allows neuroscientists to automatically extract structural connectomes from diffusion-weighted MRI data and functional connectomes from fMRI data based on a number of state-of-the-art methods for image processing, tractography reconstruction and connectome generation. Pipeline output can be directly uploaded to The Virtual Brain neuroinformatics platform for large-scale brain simulation. Further pipeline outputs include: raw tractography output (track streamlines), structural (coupling weights and distances) and functional connectomes, region-wise fMRI time series, M/EEG region-wise source activity time series. The pipeline supports the following atlasses: AAL, AAL2, Craddock200, Craddock400, Desikan Killiany, Destrieux, Human Connectome Project Multimodal Parcellation and Perry512. The pipeline is available as a Docker container based on the BIDS MRtrix3 App containing environment and software for connectome extraction (e.g. FreeSurfer, FSL, MRtrix). The container makes use of parallelized software that can be run with multiple threads locally or on supercomputers. Input data must be provided in BIDS format. As a minimum, dwMRI and strucutral MRI scans need to be provided. In addition, the pipeline can process fMRI (region-wise fMRI time courses and functional connectomes), EEG and MEG data (region-wise source activity time courses).

Whole-brain simulationModelling and simulation

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