Image modelling software tools | Electrophysiology data analysis
Image-based modeling and simulation aims at using systematic, quantitative image data to build predictive models of biological systems that can be simulated with a computer. This allows one to disentangle molecular mechanisms from effects of shape and geometry. Questions like "what is the functional role of shape" or "how are biological shapes generated and regulated" can be addressed in the framework of image-based systems biology.
Simulates the dynamics of large-scale brain networks with biologically realistic connectivity. The Virtual Brain 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 The Virtual Brain 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. The Virtual Brain 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.
Accounts for the relationship between BOLD and ECoG data from human visual cortex in V1-V3. BOLD_LFP uses the model predictions and data matching in three ways: (i) across stimuli, the BOLD amplitude and ECoG broadband power were positively correlated, (ii) the BOLD amplitude and alpha power (8-13 Hz) were negatively correlated, and (iii) the BOLD amplitude and narrowband gamma power (30-80 Hz) were uncorrelated.
Interfaces standard electrophysiology data sources and collates various analysis and simulation tools. FIND allows concise review of methods and algorithms, and opens possibilities for enhancements. It offers feature for the unified data import, representation and storage allowing for a standardized interfacing, independently of the experimental hardware and software used. This tool provides effective means of quality management.
Allows to determinate the laminar origin of Magnetoencephalography (MEG) sensor activity. MEG laminar simulations permits to test theories of human cognition that involve laminar- and frequency- specific mechanisms. This tool is able to compare and evaluate analysis techniques for non-invasive laminar specific inference in human neocortex.
Generates multiple distinct oscillations corresponding to different physiological conditions. This method is a unified model of the thalamus that offers a mechanistic understanding of thalamic oscillations and supports the long-standing notion of a thalamic “pacemaker”. This tool enables users to examine the impact of rhythmic stimulation on thalamic network dynamics.
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