Debian Science Project
Summary
Electrophysiology
Debian Science - pakker for elektrofysiologi

Denne metapakke vil installere Debianpakker, som kan være nyttige for videnskabsmænd, der udfører elektrofysiologisk neurovidenskabelig forskning.

Udvalget af pakker er målrettet anvendelsen af analyseteknikker. Metodeudviklere refereres til metapakkerne science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging og med-imaging-dev for en række yderligere programmer, som kan være nyttige til elektrofysiologisk forskning.

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
??? missing short description for package libdrawtk-dev :-(
Maintainer: Nicolas Bourdaud
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libgdf-dev
IO-bibliotek for GDF'en - udviklingsbiblioteket
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GDF (General Dataformat for Biosignals) er lavet for at tilbyde et generisk lager for biosignaler, såsom EEG, ECG, MEG etc.

Denne pakke tilbyder teksthovedfilerne.

Please cite: Alois Schlögl: GDF – A general dataformat for BIOSIGNALS. The Computing Research Repository abs/cs/0608052 (2006)
sigviewer
Grafisk brugerflade-fremviser for biosignaler såsom EEG, EMG og ECG
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SigViewer er et fremvisnings- og bedømmelsesprogram for biomedicinske signaldata. Det afhænger af biosig4c++-biblioteket, som understøtter et antal dataformater (inklusive EDF, BDF, GDF, BrainVision, BCI2000, CFWB, HL7aECG, SCP_ECG (EN1064), MFER, ACQ, CNT(Neuroscan), DEMG, EGI, EEG1100, FAMOS, SigmaPLpro, TMS32). Den fuldstændige liste over understøttede filformater er tilgængelig på http://pub.ist.ac.at/~schloegl/biosig/TESTED.

Udover at vise biosignaler undestøtter SigViewer oprettelse af annotationer til at vælge artefakter eller specifikke hændelser.

Screenshots of package sigviewer

Official Debian packages with lower relevance

aghermann
Program for soveforskningseksperimenter
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Aghermann er et program designet omkring et fælles arbejdsforløb indenfor soveforskning, fuldstændig med bedømmelsesfacilitet; cairo underbilledpunktstegning på skærmen eller til en fil; konventionel PSD- og EEG Micrcontinuity-profiler; uafhængig komponentanalyse; artefaktdetekering og Process S-simulering der følger Achermann et al, 1993.

klustakwik
Automatisk sortering af eksempler (spikes) i klynger
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KlustaKwik er et program til automatisk klyngeopbygning af sammenhængende data til en blanding af Gaussians. Programmet blev oprindelig udviklet for sortering af neuronale handlingspotentialer, men kan anvendes til alle slags 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. (PubMed,eprint) Journal of Neurophysiology 84(1):401-414 (2000)
libbiosig-dev
I/O-bibliotek for biomedicinske data - udviklingsfiler
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BioSig er et bibliotek for adgang til filer i flere forskellige biomedicinske dataformater (inklusive EDF, BDF, GDF, BrainVision, BCI2000, CFWB, HL7aECG, SCP_ECG (EN1064), MFER, ACQ, CNT(Neuroscan), DEMG, EGI, EEG1100, FAMOS, SigmaPLpro, TMS32). Den fulde liste over understøttede filformater er tilgængelig på http://pub.ist.ac.at/~schloegl/biosig/TESTED .

Denne pakke tilbyder hovedfiler og det statiske bibliotek.

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
Bibliotek til enheder som registrerer biosignaler - udviklingsfiler
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Eegdev er et bibliotek som tilbyder en samlet grænseflade, der tilgår forskellige EEG-signalsystemer (og andre biosignaler). Denne grænseflade er designet til at være både fleksibel og effektiv. Den enhedsspecifikke del er implementeret gennem udvidelsesmoduler, der gør det rimelig nemt at tilføje nye enhedsmotorer, selv hvis biblioteket endnu ikke understøtter dem officielt.

Kernebiblioteket tilbyder ikke kun brugerne samlede og konsistente grænseflader til registreringsenheden, det tilbyder også mange funktioner til enhedsmotorerne, rækkende fra konfiguration af data-typekonvertering og -skalering, hvilket gør det nemt at skrive nye enhedsmotorer.

Dette bibliotek er særligt nyttigt til håndtering af registreringsdelen for en grænseflade af typen Brain Computer Interface (BCI), eller enhver realtids multi-elektrode-registreringsenhed i neurofysiologisk forskning.

Denne pakke indeholder filerne krævet for at kompilere og lænke programmer, der bruger eegdev. Pakken tilbyder også teksthovederne krævet for at udvikle nye enhedsudvidelsesmoduler. Manualsiderne og eksempler er indeholdt i denne pakke.

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
Bibliotek til at læse/skrive EEG-datafilformater - udviklingsfiler
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Xdffileio er et bibliotek, der tilbyder en ensartet grænseflade til at skrive og læse diverse biosignal-filformater i realtid (dvs. udsendelser). Er blevet designet til at tilbyde en fleksibel, konsistent og generisk grænseflade til alle understøttede filformater, mens den minimerer belastningen funktionen kalder: de tungeste operationer (type casting, skalering og formatering) frakobles i en separat tråd. Dette design gør det specielt egnet til direkte brug i en dataindhentelsesløkke (som i elektrofysiologi-optagelse eller i Brain-Computer Interfaces (BCI)).

Genericiteten for grænsefladen udfører diverse trivielle operationer såsom transformation af en optaget fil eller dets konvertering til et andet filformat. Xdffleio understøtter i øjeblikket filformaterne EDF, BDF, GDF1 og GDF2 og flere vil blive tilføjet i fremtiden.

Denne pakke indeholder filerne krævet til at kompilere og henvise programmer, der bruger xdffileio.

python3-bioxtasraw
Behandl biologiske plotdata med lille vinkel
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BioXTAS RAW er et Pythonprogram, baseret på en grafisk brugerflade, til reduktion og analyse af lille-vinkel røntgenplotdata (SAXS). Pakken er designet for biologiske SAXS-data.

BioXTAS RAW tilbyder et alternativ til lukkede kildeprogrammer såsom Primus og Scatter for primær dataanalyse. Da programmet kan kalibrere, maskere og integrere billeder, så er det også et alternativ til synchroton beamline-datakanaler, som videnskabsfolk kan installere på deres egen computer og bruge både hjemme og ved beamline.

python3-neo
Python IO-bibliotek for elektrofysologiske dataformater
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NEO står for Neural Ensemble Objects og er et projekt, der tilbyder fælles klasser og koncepter for håndtering af elektrofysiologiske (in vivo og/eller simulerede) data til at facilitere samarbejdende program/algoritme-udvikling. Specifikt tilbyder Neo: et sæt af klasser med datarepræsentation med præcise definitioner, et IO-modul med en simpel API, dokumentation og et sæt af eksempler.

NEO tilbyder understøttelse for læsning af data fra utallige proprietære filformater (f.eks. Spike2, Plexon, AlphaOmega, BlackRock, Axon), understøttelse af læs/skriv for diverse åbne formater (f.eks. KlustaKwik, Elan, WinEdr, WinWcp, PyNN) samt understøttelse for gængse filformater, såsom HDF5 med Neo-struktureret indhold (NeoHDF5, NeoMatlab).

Neo's IO-faciliteter kan ses som en pure-Python og open-source Neuroshare-erstatning.

science-dataacquisition
Debian Science - dataindhentelsespakker
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Denne metapakke vil installere Debian Science-pakker relateret til dataindhentelse. Dette kan bruges indenfor flere videnskaber (som for eksempel science-viewing og science-typesetting).

science-neuroscience-modeling
Debian Science - pakker til modellering af neurale systemer
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Denne metapakke vil installere Debianpakker, som kan være nyttige for videnskabsmænd interesseret i modellering af neurale netværkssystemer på forskellige niveauer (fra en enkel neuron til komplekse netværk).

Udvalget af pakker er målrettet anvendelsen af simuleringsteknikker. Metoder som udviklere refereres til er metapakkerne science-statistics, science-imageanalysis, science-numericalcomputation, med-imaging, og med-imaging-dev for en række yderligere programmer, som kan være nyttige indenfor neurovidenskabelig forskning.

stimfit
Program til visning og analyse af elektrofysiologiske data
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Stimfit er et gratis, hurtigt og simpelt program til visning og analyse af elektrofysiologiske data. Den er udstyret med en indlejret Pythonskal, som giver dig mulighed for at udvide programmets funktionalitet ved hjælp af numeriske biblioteker såsom NumPy og 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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Version: 0.0-1

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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Version: 0.0-1

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 248069