Task: Electrophysiology
Install: false
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

Recommends: openelectrophy

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

Suggests: klustakwik

Recommends: libgdf-dev

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.

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.

Suggests: stimfit

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++.

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.

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

Suggests: libbiosig-dev

Recommends: sigviewer

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

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

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

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

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.

Suggests: neo
Homepage: http://neuralensemble.org/trac/neo
Language: Python
WNPP: 659691
Responsible: NeuroDebian Team <team@neuro.debian.net>
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.

Suggests: python3-neo

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.

Recommends: libdrawtk-dev

Suggests: libxdffileio-dev

Suggests: librtfilter-dev

Suggests: libeegdev-dev

Suggests: libmcpanel-dev

Suggests: eegview

Suggests: aghermann

Suggests: python3-bioxtasraw

Suggests: eeglab
Homepage: http://sccn.ucsd.edu/eeglab
Language: C, Matlab/Octave
WNPP: 605739
Responsible: NeuroDebian Team <team@neuro.debian.net>
License: GPL-2+
Pkg-URL: http://neuro.debian.net
Pkg-Description: toolbox for processing and visualization of electrophysiological data
 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.
Published-Authors: Delorme A and Makeig S
Published-In: Journal of Neuroscience Methods 134:9-21
Published-Title: EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics
Published-Year: 2004
Registration: http://sccn.ucsd.edu/eeglab/install.html

#Suggests: python-neuroshare

Suggests: patchclamp
Homepage: http://sourceforge.net/projects/patchclamp
Language: C/C++
Responsible: Vadim Alexeenko <v.a.alexeenko@gmail.com>
License: GPL-2+
Pkg-Description: recorder of single-channel and whole-cell currents
 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

Suggests: spykeview
Homepage: https://github.com/rproepp/spykeviewer
Language: Python
WNPP: 687703
License: promised MIT or BSD-3
Pkg-Description: GUI application for navigating, analyzing and visualizing electrophysiological datasets
 Based on the neo framework, it works with a wide variety of data
 formats.  Plugin interfaces allow for rapid extension with custom
 analyses.
Remark: Upstream promises public release by SfN 2012 in October