Debian Science Electrophysiology packages

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.

GDF (General Dataformat for Biosignals) er lavet for at tilbyde et generisk lager for biosignaler, såsom EEG, ECG, MEG etc.

Denne pakke tilbyder teksthovedfilerne.

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.

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 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.

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.

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.

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.

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.

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.

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.

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

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 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.

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.

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 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

This package provides the startup script for the OpenElectrophy GUI.

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.

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

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).

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.

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

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.

 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.

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.

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.

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 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.

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.

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

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.

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++.