Task: Electrophysiology
Description: 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.

Suggests: science-neuroscience-modeling

Suggests: science-dataacquisition


Depends: openelectrophy
Homepage: http://packages.python.org/OpenElectrophy
License: Cecill v2 (GPL-compatible)
Language: Python
Responsible: NeuroDebian Team <team@neuro.debian.net>
WNPP: 556552
Published-Title: OpenElectrophy: an electrophysiological data- and analysis-sharing framework
Published-Authors: Samuel Garcia* and Nicolas Fourcaud-Trocmé
Published-In: Frontiers in Neuroinformatics, 3:14
Published-Year: 2009
Published-DOI: 10.3389/neuro.11.014.2009
Pkg-Description: data analysis framework for intra- and extra-cellular recordings
 This package provide a library und GUI for analyzing electrophysiological
 data. The data handling and storage uses a MySQL-server. The package is written
 in pure Python.

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Suggests: spike
Homepage: http://neuroanalysis.org
Language: C++, Octave/Matlab
Responsible: NeuroDebian Team <team@neuro.debian.net>
License: BSD-3 and Academic Free License
Pkg-Description: spike train analysis toolbox
 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.
Published-Authors: David H. Goldberg, Jonathan D. Victor, Esther P. Gardner, and Daniel Gardner
Published-DOI: 10.1007/s12021-009-9049-y
Published-In: Neuroinformatics, 7, 165–178
Published-Title: Spike Train Analysis Toolkit: Enabling Wider Application of Information-Theoretic Techniques to Neurophysiology
Published-Year: 2009

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Suggests: klustakwik
Published-Authors: Kenneth D. Harris, Darrell A. Henze, Jozsef Csicsvari, Hajime Hirase, and György Buzsáki
Published-In: Journal of Neurophysiology, 84, 401-414
Published-Title: Accuracy of Tetrode Spike Separation as Determined by Simultaneous Intracellular and Extracellular Measurements
Published-Year: 2000

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Depends: libgdf-dev
Homepage: http://sourceforge.net/projects/libgdf
Language: C++, Octave/Matlab
WNPP: 601707
Responsible: NeuroDebian Team <team@neuro.debian.net>
License: LGPL-3
Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/libgdf.git
Vcs-Git: git://git.debian.org/git/pkg-exppsy/libgdf.git
Pkg-URL: http://neuro.debian.net/pkgs/libgdf-dev.html
Pkg-Description: IO library for the GDF -- development library
 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.

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Suggests: neurodata
Homepage: http://sourceforge.net/projects/neurodata/
Language: C++, Octave/Matlab, Perl
License: GPL-2+
Pkg-Description: suite to analyze data acquired from electrophysiology experiments
 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.

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Suggests: qrtailab
Why: Useful and used in acquisition/analysis setups
Homepage: http://qrtailab.sourceforge.net/
License: LGPL-2
Pkg-Description: Qt-GUI for RTAI
 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.

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Suggests: stimfit

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Suggests: trellis-neuro
Homepage: http://sourceforge.net/projects/trellis-neuro/
Language: C, C++
License: GPL-3+ and LGPL-3+
Pkg-Description: interface to neurophysiology data acquisition and stimulation instruments
 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++.

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Suggests: relacs
Homepage: http://www.relacs.net
Language: C++
WNPP: 604564
License: GPL-2+
Pkg-Description: framework for closed-loop neurophysiological experiments
 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.

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Suggests: chronus
Homepage: http://www.chronux.org/
Language: C, Matlab/Octave
License: GPL-2+
Pkg-Description: platform for analysis of neural signals
 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.
Registration: http://www.chronux.org/register/
Remark: last release more than 2 years ago, and no major vital signs since then

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Suggests: libbiosig0
Published-Authors: Alois Schlögl, Clemens Brunner
Published-DOI: 10.1109/MC.2008.407
Published-In: Computer, 41(10): 44-50
Published-Title: BioSig: A Free and Open Source Software Library for BCI Research
Published-URL: http://pub.ist.ac.at/~schloegl/publications/Schloegl2007_BCI_Software.pdf
Published-Year: 2008

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Depends: sigviewer
Homepage: http://sigviewer.sourceforge.net
Language: C++
WNPP: 585535
Responsible: NeuroDebian Team <team@neuro.debian.net>
License: GPL-3+
Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/sigviewer.git;a=summary
Vcs-Git: git://git.debian.org/pkg-exppsy/sigviewer.git
Pkg-URL: http://neuro.debian.net/pkgs/sigviewer.html
Pkg-Description: GUI viewer for biosignals such as EEG, EMG, and ECG
 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.

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Suggests: nspike
Homepage: http://nspike.sourceforge.net
Language: C++
License: GPL-2+
Pkg-Description: electrophysiological and behavioral data collection
 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: Last vital signs from 2 years ago

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Suggests: rtxi
Homepage: http://www.rtxi.org
Language: C++
License: GPL-2+
Pkg-Description: real-time data acquisition and control applications in biological research
 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

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Suggests: bluespike
Homepage: https://github.com/globalvariable/BlueSpike
Language: C
WNPP: 611211
License: GPL-2+
Pkg-Description: Data Acquisition and Neural Spike Processing Software
 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
Published-Authors: Mehmet Kocaturk <kocaturk@gmail.com> et al.
Published-In: SfN2010, Poster 818.22/OOO43
Published-Title: Real-time experimental interface for electrophysiology experiments
Published-Year: 2010

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Suggests: meabench
Homepage: http://www.its.caltech.edu/~daw/meabench/
Language: C++
WNPP: 611363
License: GPL-2+
Pkg-Description: tools for recording from MEAs and RT processing
 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).
Published-Authors: D. A. Wagenaar, T. B. DeMarse, and S. M. Potter
Published-In: Proc. 2nd Int. IEEE EMBS Conf. Neural Eng., 518–521
Published-Title: MEABench: A Toolset for Multi-electrode Data Acquisition and On-line Analysis
Published-URL: http://www.its.caltech.edu/~daw/abstracts/05-WDP.html
Published-Year: 2005
Remark: 64-bit port is not yet fully tested/supported

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Suggests: mclust
Homepage: http://redishlab.neuroscience.umn.edu/MClust/MClust.html
Language: C/C++, Matlab
License: non-DFSG (restrictions: modifications, attribution)
Pkg-Description: Matlab toolbox for clustering of electrophysiologic recordings
  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.

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Suggests: neo
Homepage: http://neuralensemble.org/trac/neo
Language: Python
License: BSD
Vcs-SVN: https://neuralensemble.org/svn/neo/
Pkg-Description: IO library for electrophysiological data formats in 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: Upstream says not worth packaging before v0.2 is released.

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Suggests: pymeg
Homepage: https://github.com/badbytes/pymeg/wiki
Language: Python
License: GPL-3
Pkg-Description: suite for analysis of magnetoencephalography (MEG) data
  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: Needs DFSG-ification.
        According to the author is not yet ready for the use by
        mortals -- wasn't released yet.

Depends: libdrawtk-dev
Homepage: http://cnbi.epfl.ch/software/drawtk.html
Language: C
WNPP: 646948
Responsible: Nicolas Bourdaud <nicolas.bourdaud@gmail.com>
License: LGPL-3
Vcs-Browser: http://cnbisrv02.epfl.ch/cgit/pkg-drawtk.git
Vcs-Git: git://cnbisrv02.epfl.ch:443/pkg-drawtk.git
Pkg-Description: Library to design easily visual feedback of BCI
 This package provides an C library to perform efficient 2D drawings. The
 drawing is done by OpenGL which allow us fast and nice rendering of basic
 shapes, text, images and video. It should among other provides all the
 necessary building blocks to create quickly stimuli for an experiment in
 psychophysics or to design visual feedback for BCI.

Suggests: libxdffileio-dev
Homepage: http://cnbi.epfl.ch/software/xdffileio.html
Language: C
WNPP: 646954
Responsible: Nicolas Bourdaud <nicolas.bourdaud@gmail.com>
License: LGPL-3
Vcs-Browser: http://cnbisrv02.epfl.ch/cgit/pkg-xdffileio.git
Vcs-Git: git://cnbisrv02.epfl.ch:443/pkg-xdffileio.git
Pkg-Description: Library to read/write EEG data file formats
 xdffileio provides a unified interface to read/write EEG file format
 in realtime (streaming data). It has been designed to provide a
 consistent and common interface to all supported file formats
 while minimizing the CPU cost on the main processing loop.
 It has been particularly designed to be used in a Brain Computer
 Interface (BCI).
 .
 It currently supports the following file formats: EDF, BDF, GDF 1.X, GDF 2.X

Suggests: librtfilter-dev
Homepage: http://cnbi.epfl.ch/software/rtfilter.html
Language: C
WNPP: 646956
Responsible: Nicolas Bourdaud <nicolas.bourdaud@gmail.com>
License: LGPL-3
Vcs-Browser: http://cnbisrv02.epfl.ch/cgit/pkg-rtfilter.git
Vcs-Git: git://cnbisrv02.epfl.ch:443/pkg-rtfilter.git
Pkg-Description: Multichannel realtime filtering library
 rtfilter provides a library written in C implementing realtime digital
 filtering functions optimized for multichannel signals (i.e. filtering 
 multiple signals with the same filter). The core of the library implements
 FIR and IIR filtering for float and double data type (complex or real
 data). Additional functions are also provided to design few usual filters:
 Butterworth, Chebyshev, windowed sinc, analytical filter...

Suggests: libeegdev-dev
Homepage: http://cnbi.epfl.ch/software/eegdev.html
Language: C
Responsible: Nicolas Bourdaud <nicolas.bourdaud@gmail.com>
License: LGPL-3
Pkg-Description: Library to acquire data from various EEG recording devices
 eegdev is a library that provides a unified and efficient interface for
 accessing an EEG recording system (the development targets mainly Biosemi
 and g.Tec system) and can be used as well to playback data in the software
 stack. It has been designed especially for being integrated in a BCI.
 .
 In addition, it helps the implemention of new drivers/backends by sharing
 part of code common to all of them such as type casting, scaling, exposing  
 capabilities, channels selection, error reporting...

Suggests: libmcpanel-dev
Homepage: http://cnbi.epfl.ch/software/mcpanel.html
Language: C
Responsible: Nicolas Bourdaud <nicolas.bourdaud@gmail.com>
License: GPL-3
Pkg-Description: Library providing a scope for multichannel signals
 mcpanel is a library that provides a scope interface for displaying
 multichannel signal based on Gtk+. It has been designed to implement easily
 a realtime display of signal and can be easily integrated in other projects.

Suggests: eegview
Homepage: http://cnbi.epfl.ch/software/eegview.html
Language: C
Responsible: Nicolas Bourdaud <nicolas.bourdaud@gmail.com>
License: GPL-3
Pkg-Description: Software to display/record EEG signals
 eegview is a small software to display/record EEG signals. It is 
 particularly useful when used as the acquisition part of a offline protocol 
 or for checking that electrodes are correctly placed...
