A software package running under MATLAB and allowing for analysis and visualization of functional brain networks from M/EEG recordings. The main objective of this tool is to cover the complete processing framework from the M/EEG pre-processing to the identification of the functional brain networks. EEGNET includes mainly the calculation of the functional connectivity between scalp M/EEG signals as well between reconstructed brain sources obtained from the solution of the inverse problem. It also includes the characterization of the brain networks by computing the network measures proposed in the field of graph theory. EEGNET provides user-friendly interactive 2D /3D brain networks visualization.
Assists in visualizing results of processing steps and final outputs. MNE-Python is a scripting-based package with many visualization capabilities. It covers multiple methods of data preprocessing, source localization, statistical analysis, and estimation of functional connectivity between distributed brain regions. It offers some unique capabilities, in a coherent package facilitating the combination of standard and advanced techniques in a single environment.
Processes continuous and event-related EEG (electro-encephalography) and MEG (magneto-encephalography). EEGLAB also processes other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data. EEGLAB provides an interactive graphic user interface (GUI) allowing users to flexibly and interactively process their high-density EEG and other dynamic brain data using ICA and/or time/frequency analysis, as well as standard averaging methods.
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.
Analyzes and visualizes electrophysiological data. Stimfit is a free analysis environment for cellular neurophysiology. This tool can number and clarify the activity of single neurons and communication between neurons. It contains algorithms to characterize the kinetics of presynaptic action potentials. This software uses several typical formats for biomedical signals, including those most commonly used in cellular electrophysiology.
Analyzes, browses and analyzes data from electrophysiology experiments or neural simulations. Spyke Viewer is built on an object model for electrophysiology data: the Neo library. This software furnishes a central graphic user interface from which independently developed analysis can be executed. It provides a flexible plugin architecture that permits creation of new plugins to allow extensibility.
Permits to visualize electrodes implantation on image data and prepares database for group studies. IntrAnat Electrodes allows users to search across patients according to a variety of anatomical and functional criteria. It uses established research neuroimaging toolboxes such as BrainVisa, Freesurfer, SPM and ANTs to recycle optimal and validated image analysis processes.
Visualizes cortical activations on a three-dimensional (3D) model of a brain surface. NeuralAct provides researchers working with Electrocorticography (ECoG) the means to observe the activity on models of the cortex. It includes a model of a pial cortical surface in the Talairach coordinate space derived from the AFNI SUMA package. This method is robust and easy to use, and should therefore benefit a wide range of researchers in cortical surface areas.
Uses as a viewer for continuously recorded signals, spiking activity, and behavioral events. NeuroScope is an advanced viewer for electrophysiological and behavioral data with limited editing capabilities. NeuroScope displays the data in a trace view (electrophysiological signals) and optionally a position view (position tracking) combined in a display. NeuroScope is a part of the Neurosuite, a package designed to help neurophysiologists process and view recorded data in an efficient and user-friendly manner.
Creates 3D PDF documents for biomedical publications. MeVisLab aims to facilitate the generation of U3D files by reducing the number of necessary tools to only one application in the field of biomedical image processing. It allows users to build sophisticated applications with graphical user interfaces that hide the underlying platform and do not require substantial programming knowledge. This tool permits simple assembling of image processing networks.
A MATLAB-based toolbox, eConnectome (electrophysiological connectome), for mapping and imaging functional connectivity at both the scalp and cortical levels from the electroencephalogram (EEG), as well as from the electrocorticogram (ECoG). Graphical user interfaces were designed for interactive and intuitive use of the toolbox. Major functions of eConnectome include EEG/ECoG preprocessing, scalp spatial mapping, cortical source estimation, connectivity analysis, and visualization. Granger causality measures such as directed transfer function and adaptive directed transfer function were implemented to estimate the directional interactions of brain functional networks, over the scalp and cortical sensor spaces. Cortical current density inverse imaging was implemented using a generic realistic geometry brain-head model from scalp EEGs. Granger causality could be further estimated over the cortical source domain from the inversely reconstructed cortical source signals as derived from the scalp EEG.
Allows visualization and processing of electrophysiological signals. AnyWave is composed of several components: a visualization component that is the graphic user interface; another is a montage manager for editing user-defined montage; events can be handled by the markers manager component; the process manager exploits optional signal processing algorithm modules and finally a component deals with the plugin compatibility. It supports plugin modularity with the possibility to add plugins to add new features such as compatibility with other formats.
Assists users in providing heart rate variability analysis. RHRV provides utility functions for importing heart rate time series data, analyzing their variability, and plotting and/or exporting the analysis results. It uses a custom data structure to store all information related to digital recordings from a polysomnograph. It also includes functions for loading ASCII or WFDB formatted files.
Allows neuroscientists to investigate the major cluster evolution patterns over space and time. ECoG ClusterFlow is a hierarchical multi-scale approach that supports the exploration, comparison and analysis of time-varying community evolution patterns at varying temporal granularity. It provides (i) an overview that summarizes the overall changes in cluster evolution, where users explore salient dynamic patterns; and (ii) a hierarchical glyph-based timeline visualization for exploring the dynamic spatial organizational changes of the clusters that uses data aggregation and small multiples methods.
Provides a toolbox for electrophysiological data analysis. NeoAnalysis is based on the Neo package to standardize electrophysiological data. This software is composed of six main modules that: (1) converts recording files different data acquiring systems to standardized format (HDF5); (2) detects spikes the raw signals; (3) sorts offline spike; (4) filters analog signals; (5) analyzes data at the population level and (6) displays data and analysis results.
A Matlab-based software for the visualization of multi-channel biomedical signals, particularly for the electroencephalography (EEG). BioSigPlot is designed for researchers on both engineering and medicine who should collaborate, visualize and analyze signals. It aims to provide a highly customizable interface for signal processing experimentation in order to plot several kinds of signals while integrating the common tools for physician. The main advantages compared to other existing programs are the multi-dataset displaying, the synchronization with video and the online processing.
Allows users to inspect and mark multi-channel digitized contents with no constraint concerning marking periods of data in subsets of channels. The EyeBallGUI interface simplifies users the management and the annotation of their experiments. Its flexibility allows the retention of more good quality bio-signal data and it facilitates marking of multi-channel bio-signals for other purposes not readily supported by existing toolboxes.
Offers a digital imaging and communications in medicine (DICOM) solution. OsiriX is an image processing software that provides displaying, reviewing, interpreting and post-processing image files. It supports DICOM standard for a complete integration in a workflow environment and in a picture archiving and communication system (PACS).
Allows users to view clinical images. WEASIS is a software consisting of a multipurpose web-based viewer and dealing with digital imaging and communications in medicine (DICOM) dataset. It supplies different types of image in an application that can be run as a Java platform independent stand-alone application and stored on a DVD along with a data set.
Creates annotations to select artifacts or specific events. Sigviewer is an application for biosignals, designed to display electroencephalographic (EEC) and other biosignal data. This tool can include basic signal processing modules such as computing the average over selected epochs.
Allows users to display medical images in digital imaging and communications in medicine (DICOM) format. Jivex DICOM Viewer offers an interactive interface to manipulate different types of medical images.
Converts DICOM ECG files to multiple format types. DICOM ECG Viewer can support a lot of output format such as pdf, eps, jpeg, png and more. A trial version is available online allowing users to test software functionalities.
Provides a method for Heart Rate Variability (HRV) analysis. HRV toolkit is a rigorously validated package of open source including visualization of normal sinus (NN) interval time series, automated outlier removal, and calculation of the basic time- and frequency-domain HRV statistics widely used in the literature.
Enables objects visualization and handling for medical imaging. Anatomist is one of the BrainVisa suite’s softwares. Features are based on management of several types of objects, management of coordinate systems and transformations, possibility of building complex 3D scenes with several objects of any type and tools such as color palettes, region of interest module, or mathematic morphology.
Permits to store and display timeseries files. EDFbrowser supports Electroencephalogram (EEG), Electromyogram (EMG), Electrocardiogram (ECG), or BioImpedance files such as other type of timeseries files. It allows Z-EEG measurement and precise measurements by using crosshairs. The tool provides an annotation editor, a header editor and zoom functions. It permits to fix the EDF-header in case where the value for digital maximum is lower than digital minimum.
Assists users in managing clinical, demographic and biomolecular patient data collected during clinical trials. AGUIA provides a formal, automatable bridge between resource description framework (RDF) documents and the browser’s document object model (DOM)-centric extensible syntax. It allows the clinical/domain user’s requests and their replies to be automatically translated into graphic interfaces.
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