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| Written in | Python |
|---|---|
| Operating system | All OS supported by Python |
| Available in | English |
| Type | Neuroimaging software |
| Website | mne |
MNE-Python ("MNE") is an open source toolbox for EEG and MEG signal processing. [1] It is written in Python and is available from the PyPI package repository. [2]
Source separation, blind signal separation (BSS) or blind source separation, is the separation of a set of source signals from a set of mixed signals, without the aid of information about the source signals or the mixing process. It is most commonly applied in digital signal processing and involves the analysis of mixtures of signals; the objective is to recover the original component signals from a mixture signal. The classical example of a source separation problem is the cocktail party problem, where a number of people are talking simultaneously in a room, and a listener is trying to follow one of the discussions. The human brain can handle this sort of auditory source separation problem, but it is a difficult problem in digital signal processing.
Magnetoencephalography (MEG) is a functional neuroimaging technique for mapping brain activity by recording magnetic fields produced by electrical currents occurring naturally in the brain, using very sensitive magnetometers. Arrays of SQUIDs are currently the most common magnetometer, while the SERF magnetometer is being investigated for future machines. Applications of MEG include basic research into perceptual and cognitive brain processes, localizing regions affected by pathology before surgical removal, determining the function of various parts of the brain, and neurofeedback. This can be applied in a clinical setting to find locations of abnormalities as well as in an experimental setting to simply measure brain activity.
Orange is an open-source data visualization, machine learning and data mining toolkit. It features a visual programming front-end for explorative rapid qualitative data analysis and interactive data visualization.
The following tables provide a comparison of numerical-analysis software.
EEGLAB is a MATLAB toolbox distributed under the free BSD license for processing data from electroencephalography (EEG), magnetoencephalography (MEG), and other electrophysiological signals. Along with all the basic processing tools, EEGLAB implements independent component analysis (ICA), time/frequency analysis, artifact rejection, and several modes of data visualization. EEGLAB allows users to import their electrophysiological data in about 20 binary file formats, preprocess the data, visualize activity in single trials, and perform ICA. Artifactual ICA components may be subtracted from the data. Alternatively, ICA components representing brain activity may be further processed and analyzed. EEGLAB also allows users to group data from several subjects, and to cluster their independent components.
QtiPlot is a cross-platform computer program for interactive scientific graphing and data analysis. It is similar to the proprietary programs Origin or SigmaPlot.
The Donders Centre for Cognitive Neuroimaging is one of the four centers which together comprise the Donders Institute. It is located at the campus of the Radboud University Nijmegen and maintains strong ties with the Max Planck Institute for Psycholinguistics. It is named after the Dutch ophthalmologist Franciscus Donders, who was the first scientist to use differences in reaction times to infer differences in cognitive processing.
Chronux is an open-source software package developed for the loading, visualization and analysis of a variety of modalities / formats of neurobiological time series data. Usage of this tool enables neuroscientists to perform a variety of analysis on multichannel electrophysiological data such as LFP, EEG, MEG, Neuronal spike times and also on spatiotemporal data such as FMRI and dynamic optical imaging data. The software consists of a set of MATLAB routines interfaced with C libraries that can be used to perform the tasks that constitute a typical study of neurobiological data. These include local regression and smoothing, spike sorting and spectral analysis - including multitaper spectral analysis, a powerful nonparametric method to estimate power spectrum. The package also includes some GUIs for time series visualization and analysis. Chronux is GNU GPL v2 licensed.
Electroencephalography (EEG) is a method to record an electrogram of the electrical activity on the scalp that has been shown to represent the macroscopic activity of the surface layer of the brain underneath. It is typically non-invasive, with the electrodes placed along the scalp. Electrocorticography, involving invasive electrodes, is sometimes called "intracranial EEG".
In computer science, Orfeo Toolbox (OTB) is a software library for processing images from Earth observation satellites.
This is a list of free and open-source software for geophysical data processing and interpretation. The list is split into broad categories, depending on the intended use of the software and its scope of functions.
FieldTrip is a MATLAB software toolbox for magnetoencephalography (MEG) and electroencephalography (EEG) analysis. It is developed at the Donders Institute for Brain, Cognition and Behaviour at the Radboud University Nijmegen, together with collaborating institutes. The development of FieldTrip is supported by funding from the BrainGain, Human Connectome and ChildBrain projects. The FieldTrip software is released as open source under the GNU General Public License.
The Neurophysiological Biomarker Toolbox (NBT) is an open source MATLAB toolbox for the computation and integration of neurophysiological biomarkers. The NBT toolbox has so far been used in seven peer-reviewed research articles, and has a broad user base of more than 1000 users. The NBT toolbox provides unique features for analysis of resting-state EEG or MEG recordings. NBT offers a pipeline from data storage to statistics including artifact rejection, signal visualization, biomarker computation, statistical testing, and biomarker databasing. NBT allows for easy implementation of new biomarkers, and incorporates an online wiki that aims at facilitating collaboration among NBT users including extensive help and tutorials. The standardised way of data storage and analysis that NBT proposes allow different research projects to merge, compare, or share their data and biomarker algorithms.
Corticocortical coherence is referred to the synchrony in the neural activity of different cortical brain areas. The neural activities are picked up by electrophysiological recordings from the brain. It is a method to study the brain's neural communication and function at rest or during functional tasks.
NeuroKit ("nk") is an open source toolbox for physiological signal processing. The most recent version, NeuroKit2, is written in Python and is available from the PyPI package repository. As of June 2022, the software was used in 94 scientific publications. NeuroKit2 is presented as one of the most popular and contributor-friendly open-source software for neurophysiology based on the number of downloads, the number of contributors, and other GitHub metrics.
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