Debian Science Project
Summary
Electrophysiology
Debian Science packages for Electrophysiology

This metapackage will install Debian packages which might be useful for scientists doing electrophysiology-based neuroscience research.

The selection of packages is targeting the application of analysis techniques. Methods developers are referred to the science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging, and med-imaging-dev metapackages for a variety of additional software that might be useful for electrophysiology research.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Science to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Science mailing list

Links to other tasks

Debian Science Electrophysiology packages

Official Debian packages with high relevance

Libdrawtk-dev
Library to simple and efficient 2D drawings (development files)
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This package provides an C library to perform efficient 2D drawings. The drawing is done by OpenGL allowing fast and nice rendering of basic shapes, text, images and videos. It has been implemented as a thin layer that hides the complexity of the OpenGL library.

This package contains the files needed to compile and link programs which use drawtk.

Libgdf-dev
IO library for the GDF -- development library
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GDF (General Dataformat for Biosignals) is intended to provide a generic storage for biosignals, such as EEG, ECG, MEG etc.

This package provides the header files and static library.

Sigviewer
GUI viewer for biosignals such as EEG, EMG, and ECG
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SigViewer is a viewing and scoring software for biomedical signal data. It relies on biosig4c++ library which supports a number of data formats (including EDF, BDF, GDF, BrainVision, BCI2000, CFWB, HL7aECG, SCP_ECG (EN1064), MFER, ACQ, CNT(Neuroscan), DEMG, EGI, EEG1100, FAMOS, SigmaPLpro, TMS32). The complete list of supported file formats is available at http://pub.ist.ac.at/~schloegl/biosig/TESTED .

Besides displaying biosignals, SigViewer supports creating annotations to select artifacts or specific events.

Screenshots of package sigviewer

Official Debian packages with lower relevance

Aghermann
Sleep-research experiment manager
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Aghermann is a program designed around a common workflow in sleep-research, complete with scoring facility; cairo subpixel drawing on screen or to file; conventional PSD and EEG Micrcontinuity profiles; Independent Component Analysis; artifact detection; and Process S simulation following Achermann et al, 1993.

Klustakwik
automatic sorting of the samples (spikes) into clusters
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KlustaKwik is a program for automatic clustering of continuous data into a mixture of Gaussians. The program was originally developed for sorting of neuronal action potentials, but can be applied to any sort of data.

Please cite: Kenneth D. Harris, Darrell A. Henze, Jozsef Csicsvari, Hajime Hirase, and György Buzsáki: Accuracy of Tetrode Spike Separation as Determined by Simultaneous Intracellular and Extracellular Measurements (2000)
Libbiosig-dev
I/O library for biomedical data - development files
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BioSig is a library for accessing files in several biomedical data formats (including EDF, BDF, GDF, BrainVision, BCI2000, CFWB, HL7aECG, SCP_ECG (EN1064), MFER, ACQ, CNT(Neuroscan), DEMG, EGI, EEG1100, FAMOS, SigmaPLpro, TMS32). The complete list of supported file formats is available at http://pub.ist.ac.at/~schloegl/biosig/TESTED .

This package provides header files and static library.

Please cite: Alois Schlögl and Clemens Brunner: BioSig: A Free and Open Source Software Library for BCI Research. (eprint) Computer 41(10):44-50 (2008)
Libeegdev-dev
Biosignal acquisition device library (Developement files)
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eegdev is a library that provides a unified interface for accessing various EEG (and other biosignals) acquisition systems. This interface has been designed to be both flexible and efficient. The device specific part is implemented by the mean of plugins which makes adding new device backend fairly easy even if the library does not support them yet officially.

The core library not only provides to users a unified and consistent interfaces to the acquisition device but it also provides many functionalities to the device backends (plugins) ranging from configuration to data casting and scaling making writing new device backend an easy task.

This library is particularly useful to handle the acquisition part of a Brain Computer Interface (BCI) or any realtime multi-electrode acquisition in neurophysiological research.

This package contains the files needed to compile and link programs which use eegdev. Its provides also the headers neeeded to develop new device plugins. The manpages and examples are shipped in this package.

Librtfilter-dev
realtime digital filtering library (development files)
Maintainer: Nicolas Bourdaud
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rtfilter is a library that provides a set of routines implementing realtime digital filter for multichannel signals (i.e. filtering multiple signals with the same filter parameters). It implements FIR, IIR filters and downsampler for float and double data type (both for real and complex valued signal). Additional functions are also provided to design few usual filters: Butterworth, Chebyshev, windowed sinc, analytical filter...

One of the main differences from other libraries providing digital signal processing is that the filter functions have been specifically designed and optimized for multichannel signals (from few channels to several hundred).

This package contains the files needed to compile and link programs which use rtfilter.

Libxdffileio-dev
Library to read/write EEG data file formats (development files)
Maintainer: Nicolas Bourdaud
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xdffileio is a library that provides a unified interface for writing and reading various biosignal file formats in realtime (i.e. streaming). It has been designed to provide a flexible, consistent and generic interface to all supported file formats while minimizing the overhead the function calls: the heaviest operations (type casting, scaling and formatting) are offloaded into a separated thread. This design makes its particularly suitable to be directly used in a data acquisition loop (like in electrophysiology recording or in Brain-Computer Interfaces (BCI)).

The genericity of the interface makes trivial various operations like transformation of a recorded file or its conversion to another file format. xdffileio currently supports EDF, BDF, GDF1 and GDF2 file formats and more will be added in future.

This package contains the files needed to compile and link programs which use xdffileio.

Python-neo
Python IO library for electrophysiological data formats
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NEO stands for Neural Ensemble Objects and is a project to provide common classes and concepts for dealing with electro-physiological (in vivo and/or simulated) data to facilitate collaborative software/algorithm development. In particular Neo provides: a set a classes for data representation with precise definitions, an IO module with a simple API, documentation, and a set of examples.

NEO offers support for reading data from numerous proprietary file formats (e.g. Spike2, Plexon, AlphaOmega, BlackRock, Axon), read/write support for various open formats (e.g. KlustaKwik, Elan, WinEdr, WinWcp, PyNN), as well as support common file formats, such as HDF5 with Neo-structured content (NeoHDF5, NeoMatlab).

Neo's IO facilities can be seen as a pure-Python and open-source Neuroshare replacement.

Python-neuroshare
Python interface and tools for Neuroshare
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The Neuroshare API is a standardized interface to access electrophysiology data stored in various different file formats. To do so, it uses format- specific shared libraries.

This package provides a high-level Python interface to the Neuroshare API that focuses on convenience for the user and enables access to all available metadata and data. The data is returned in NumPy arrays, which provides a quick route to further examination and analysis.

In addition, this package contains the ns2hdf converter tool that converts neuroshare-compatible files into the HDF5 (Hierarchical Data Format, ver. 5) file format.

Python-spykeutils
utilities for analyzing electrophysiological data
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spykeutils is a Python library for analyzing and plotting data from neurophysiological recordings. It can be used by itself or in conjunction with Spyke Viewer, a multi-platform GUI application for navigating electrophysiological datasets.

Science-dataacquisition
Debian Science data acquisition packages
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This metapackage will install Debian Science packages related to data acquisition. This might be used in several sciences (as for instance science-viewing and science-typesetting).

Science-neuroscience-modeling
Debian Science packages for modeling of neural systems
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This metapackage will install Debian packages which might be useful for scientists interested in modeling of real neural systems at different levels (from single neuron to complex networks).

The selection of packages is targeting the application of simulation techniques. Methods developers are referred to the science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging, and med-imaging-dev metapackages for a variety of additional software that might be useful for neuroscience research.

Stimfit
Program for viewing and analyzing electrophysiological data
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Stimfit is a free, fast and simple program for viewing and analyzing electrophysiological data. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy.

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Packaging has started and developers might try the packaging code in VCS

Eegview
Software to display EEG data in realtime
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This software allows one to display EEG signal in realtime as well as record them. It is the minimal recording panel needed to do simple experiment.

Libmcpanel-dev
Library to display multichannel data in realtime (Developement files)
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This package provides a library written in C implementing a set of widgets designed to view in realtime multichannels signals. Despite it has been initially design to view signals coming from a BIOSEMI Activetwo EEG system, it is totally system agnostic and any user of other system might find it useful.

This package contains the files needed to compile and link programs which use mcpanel

Neo - wnpp
IO library for electrophysiological data formats in Python
Responsible: NeuroDebian Team
License: BSD
Debian package not available
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Language: Python

NEO stands for Neural Ensemble Objects and is a project to provide common class names and concepts for dealing with electro-physiological (in vivo and/or simulated) data with the aim of getting OpenElectrophy, NeuroTools, G-node and maybe other projects with similar goals more close together.

In particular Neo provides:

  • a set a classes with precise definitions
  • an IO module that offer a simple API that fit many formats
  • documentation.
  • a set of examples like a format convertor
Remark of Debian Science team: Upstream says not worth packaging before v0.2 is released.
Openelectrophy
data analysis GUI for intra- and extra-cellular recordings
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This package provides the startup script for the OpenElectrophy GUI.

Please cite: Samuel Garcia and Nicolas Fourcaud-Trocmé: OpenElectrophy: an electrophysiological data- and analysis-sharing framework. Frontiers in Neuroinformatics 3:14 (2009)

Unofficial packages built by somebody else

Eeglab
toolbox for processing and visualization of electrophysiological data
Responsible: NeuroDebian Team
License: GPL-2+
Language: C, Matlab/Octave

EEGLAB is an interactive Matlab toolbox for processing continuous and event-related EEG, MEG and 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.

Please register by following this link if you are using eeglab.
Please cite: Delorme A and Makeig S: EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics (2004)

No known packages available but some record of interest (WNPP bug)

Bluespike - wnpp
Data Acquisition and Neural Spike Processing Software
License: GPL-2+
Debian package not available
Language: C

BlueSpike is an electrophysiology tool to perform real-time data acquisition, visualization and sorting of neuronal spikes. It continuously acquires data every 1 ms and realizes digital signal processing on retrieved data. Contains four components:

  • KernelSpike: a kernel module.
  • SpikeViewever
  • SpikeSorter
  • Channel Reviewer
Please cite: Mehmet Kocaturk <kocaturk@gmail.com> et al.: Real-time experimental interface for electrophysiology experiments (2010)
Meabench - wnpp
tools for recording from MEAs and RT processing
License: GPL-2+
Debian package not available
Language: C++

Meabench is a set of interacting linux programs for recording data from MEAs and real time processing. It can be used to acquire and visualize data from MultiChannel Systems multi-electrode array hardware in real time. On-line spike detection is available, as well as suppression of artifacts induced by 60 Hz pickup and by stimulation. A growing number of small utilities for data analysis is included with the source code, and you can easily add your own. Meabench provides continuous and triggered recording of raw electrode data as well as extracted spike data. Meabench is very suitable for real-time feedback stimulation, since roundtrip times from pre-amplifier to stimulator is less than 200 ms worst-case (less than 50 ms average).

Please cite: D. A. Wagenaar, T. B. DeMarse, and S. M. Potter: MEABench: A Toolset for Multi-electrode Data Acquisition and On-line Analysis. (2005)
Remark of Debian Science team: 64-bit port is not yet fully tested/supported
Relacs - wnpp
framework for closed-loop neurophysiological experiments
License: GPL-2+
Debian package not available
Language: C++

RELACS is designed as an framework for closed-loop experiments that may considerably speed up this traditional approach and in addition offers novel experimental possibilities. In a closed-loop experiment a stimulus is presented, the resulting response is immediately analyzed, and properties of the next stimulus (e.g. mean intensity) are adjusted as needed.

RELACS comes with an extensive set of data-analysis functions. The functions are implemented in C++ to allow fast and memory efficient data-analysis as it is required for closed-loop experiments:

  • Basic statistics (e.g. mean, standard deviation)
  • Spectral analysis: power spectrum, transfer function, coherence
  • Linear and nonlinear fits (Levenberg-Marquardt and Simplex)
  • Peak detection
  • Histograms, interpolation
  • Stimulus generation: pulse, saw tooth, band-pass filtered white noise, Ornstein-Uhlenbeck noise
  • Firing rates: mean, binned, convolved with kernels (e.g. rectangle, triangle, Gaussian)
  • Interspike intervals: histogram, CV, serial correlation, etc.
  • Spike timing precision: vector strength, reliability, correlation, synchrony etc.

RELACS plugin infrastructure allows to adapt it to specific hardware drivers and they allow you to implement research protocols, filters, spike detectors, etc.

Spykeview - wnpp
GUI application for navigating, analyzing and visualizing electrophysiological datasets
License: promised MIT or BSD-3
Debian package not available
Language: Python

Based on the neo framework, it works with a wide variety of data formats. Plugin interfaces allow for rapid extension with custom analyses.

Remark of Debian Science team: Upstream promises public release by SfN 2012 in October

No known packages available

Chronus
platform for analysis of neural signals
License: GPL-2+
Debian package not available
Language: C, Matlab/Octave

Chronux is a Matlab toolbox for signal processing of neural time series data, several specialized mini-packages for spike sorting, local regression, audio segmentation and other tasks. It also includes a graphical user interface (GUI). The current version of the GUI contains a number of features specialised to the analysis of electroencephalography (EEG) data. The eventual aim is to provide domain specific user interfaces (UIs) for each experimental modality, along with corresponding data management tools.

Please register by following this link if you are using chronus.
Remark of Debian Science team: last release more than 2 years ago, and no major vital signs since then
Mclust
Matlab toolbox for clustering of electrophysiologic recordings
License: non-DFSG (restrictions: modifications, attribution)
Debian package not available
Language: C/C++, Matlab
 MClust is a toolbox which enables a user to perform automated and
 manual clustering on single-electrode, stereotrode, and tetrode
 recordings. It allows manual corrections to automated clustering
 results. It outputs t-files, which contain (after a header) a list
 of timestamps in binary format. Timestamps are 32-bit longs at a
 resolution of 10 timestamps/ms.
Neurodata
suite to analyze data acquired from electrophysiology experiments
License: GPL-2+
Debian package not available
Language: C++, Octave/Matlab, Perl

Currently, neurodata has an Octave/MATLAB program to analyze electroneurogram traces of coupled oscillators, and a Perl library for the analysis of voltage trace data.

Nspike
electrophysiological and behavioral data collection
License: GPL-2+
Debian package not available
Language: C++

This project is a electrophysiological and behavioral data collection program that can distribute data collection tasks across multiple machines. It is designed to interface with the NSpike hardware system.

Remark of Debian Science team: Last vital signs from 2 years ago
Patchclamp
recorder of single-channel and whole-cell currents
Responsible: Vadim Alexeenko
License: GPL-2+
Debian package not available
Language: C/C++

The ultimate aim is to create an extremely user-friendly software to perform the most common tasks of recording single channels and whole-cell currents

Pymeg
suite for analysis of magnetoencephalography (MEG) data
License: GPL-3
Debian package not available
Language: Python
 PyMEG is a project in Python to do various neuroimaging processing
 with magnetoencephalography (MEG) data. The purpose of this project,
 is to create a suite of functions to do MEG analysis in Python.
Remark of Debian Science team: Needs DFSG-ification.
       According to the author is not yet ready for the use by
       mortals -- wasn't released yet.
Qrtailab
Qt-GUI for RTAI
License: LGPL-2
Debian package not available

QRtaiLab is a QT-based port of the software scope xrtailab of the RTAI project. It can be used as virtual oscilloscope and monitoring application for interacting with the real-time external.

Rtxi
real-time data acquisition and control applications in biological research
License: GPL-2+
Debian package not available
Language: C++

The Real-Time eXperiment Interface (RTXI) is a collaborative open-source software development project aimed at producing a real-time Linux based software system for hard real-time data acquisition and control applications in biological research.

Core functionality of RTXI gets extended via plugins, such as - Data Recorder - Virtual Dendrite - Spike-triggered Average - Phase Response Curve - Signal processing

Spike
spike train analysis toolbox
Responsible: NeuroDebian Team
License: BSD-3 and Academic Free License
Debian package not available
Language: C++, Octave/Matlab

This toolbox implements several information-theoretic spike train analysis techniques. This implementation behaves like a typical MATLAB toolbox, but the underlying computations are coded in C and optimized for efficiency.

Please cite: David H. Goldberg, Jonathan D. Victor, Esther P. Gardner, and Daniel Gardner: Spike Train Analysis Toolkit: Enabling Wider Application of Information-Theoretic Techniques to Neurophysiology. (2009)
Trellis-neuro
interface to neurophysiology data acquisition and stimulation instruments
License: GPL-3+ and LGPL-3+
Debian package not available
Language: C, C++

Trellis-Neuro is an Open Source, multi-platform application suite for interfacing with neurophysiology data acquisition and stimulation instruments. It is based on the eXtensible Instrument Processing Protocol (XIPP), QT 4, and C/C++.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 203532