from PhysioNet, the research resource for complex physiologic signals


Other Free Software

The free and open-source software listed on this page is likely to be of interest to many readers, although these packages are not currently available in PhysioToolkit. Please use the contact information below to obtain further information on these packages, since they are independent of PhysioNet; in general, we have no further information about them.

We welcome corrections and suggestions for this page; please use the link at the bottom of the page to write to us. We make this page available as a service to the creators and users of free (open-source) software.

COMKAT

COMKAT (COmpartment Model Kinetic Analysis Tool), is MATLAB software for compartmental modeling oriented to nuclear medicine applications (PET & SPECT). It supports models of a wide range of complexity including multiple injection and receptor models with saturation. It supports many image formats, including DICOM images. Using either the command line interface or the GUI, models are easily specified, solved, and used to fit experimental data. Sensitivity equations are supported. No mathematical derivations are required on the part of the user. For details, see:

Muzic RF, Cornelius S. COMKAT: Compartment Model Kinetic Analysis Tool. J Nucl Med 42:636-645 (2001).

Please visit the COMKAT home page to learn more and to download it. (No cost for academic/not-for-profit research use.)

DynClamp

The Dynamic Clamp protocol, developed by Sharp et. al. (J. Neurophysiol. 69:992-995; 1993) allows "insertion" of simulated membrane conductances in, and/or simulated synapses between, biological neurons. Until now, the protocol has been applied simultaneously to, at most, 2 neurons. Also, most commercial ADC/DAC boards possess only two analog outputs. The program DYNCLAMP4 can control up to 4 neurons in real time, dynamic clamp mode.

The PC-based software permits up to 8 (or more) Hodgkin-Huxley conductances and up to 18 synaptic connections (chemical, non-rectifier electrical and rectifier electrical). An auxiliary electronic circuit (for which complete construction details are provided) splits the usual 2 analog outputs to 4 analog command signals.

The authors provide C++ sources and MS-Windows binaries, together with a detailed user's guide on their web site. Also see:

RD Pinto, RC Elson, A Szücs, MI Rabinovitch, AI Selverston, HDI Abarbanel. Extended dynamic clamp: controlling up to four neurons using a single desktop computer and interface. Journal of Neuroscience Methods 108(1):39-48 (2001). [The full text of this article may be read by following the links from this site (registration required).]

For further information, please write to Reynaldo Pinto.

Engauge Digitizer

Engauge Digitizer is an open-source tool for extracting XY data from images (for example, recovering ECGs from paper strips). The software can run on any platform supported by the QT toolkit, including GNU/Linux, Mac OS X, MS-Windows (with limitations on supported image formats), and all versions of Unix.

For further information, please visit the Engauge Digitizer web site. (Also see the PhysioNet tutorial, Digitizing Paper ECGs and Other Plots.)

EP Limited: Open Source ECG Analysis Software

This package, written by Pat Hamilton, includes an excellent single-lead QRS detector (an improved version of the Pan-Tompkins detector) and a single-lead beat classifier. The code is written in C and uses the WFDB library to read data and write annotations in PhysioBank format.

The sources, together with a detailed implementation guide, may be downloaded from the author's web site (free registration required). Also see:

PS Hamilton, WJ Tompkins. Quantitative investigation of QRS detection rules using the MIT/BIH arrhythmia database. IEEE Trans. Biomed. Eng BME-33: 1158-1165 (1987).

For further information, please write to Pat Hamilton.

HRT (Heart Rate Turbulence)

HRT "is the physiological, bi-phasic response of the sinus node to premature ventricular contractions. It consists of a short initial acceleration followed by a deceleration of the heart rate." Software for computing and visualizing HRT is available in source form from its authors. (Note that the HRT method is patented and the software may be used "for purely scientific purposes only.")

For further information, please write to Prof. Dr. Georg Schmidt.

LastWave

LastWave is a "signal processing control language" with a Matlab-like syntax, written in C and usable on all popular platforms.

For further information, please write to the LastWave Group.

libRASCH

libRASCH provides a common interface for access to physiologic signals in a wide variety of formats, including several that are not supported by the WFDB software package. Currently, the following formats are supported: CFS, DasyLab, EDF+, ISHNE-Holter, MIT/AHA (WFDB) and Poly5/TMS32. The library is written in C and is available for Linux and Windows. The software also provides support for processing (e.g. beat detection in an ECG) and viewing the signals. This functionality and the access to the various file formats is realized with plugins.

For further information, please write to Raphael Schneider.

Open-Source Electrophysiological Toolbox (OSET)

OSET is a collection of electrophysiological data and open source software for biosignal generation, modeling, processing, and filtering, The toolbox is distributed under the GNU General Public License and may be freely used or modified under the specified terms of use. The software was written and is maintained mainly in MATLAB m-code by Reza Sameni of Shiraz University.

OSET includes:

Sources for OSET can be downloaded from oset.ir.

Software for Heart Rate Variability

This software, written primarily in Matlab m-code by Danny Kaplan and Phil Staffin, includes a set of functions for deriving a heart rate time series from beat interval data, together with additional functions for power spectrum and approximate entropy (ApEn) analysis.

For further information, please write to Danny Kaplan.

Software for Nonlinear Time-Series Analysis

This software, also written in Matlab m-code by Danny Kaplan, includes functions for generating surrogate data, nonlinear prediction, and the Kaplan delta-epsilon test for the existence of an underlying dynamical function component in a time series.

For further information, please write to Danny Kaplan.

TEMPO

TEMPO (Topographic EEG Mapping PrOgram), by Aleksandar Samardzic, is software for 3D visualization of the brain's electrical activity. TEMPO accepts EEG data in standard EDF files and creates an animated sequence of topographic maps, generated on the surface of a 3D head model, which can be rotated and examined interactively.

For further information, please write to Alex Samardzic.

TISEAN

TISEAN software for nonlinear TIme SEries ANalysis, by Rainer Hegger, Holger Kantz, and Thomas Schreiber (Institut für Physikalische und Theoretische Chemie, Universität Frankfurt (Main) and Max-Planck-Institut für Physik komplexer Systeme, Dresden), is "a software project for the analysis of time series with methods based on the theory of nonlinear deterministic dynamical systems, or chaos theory, if you prefer" (in the words of its authors).

On their web site, the authors provide sources written in C and Fortran, and binaries for Linux (i86), OSF1 (Alpha), and MS-Windows. Also see:

R. Hegger, H. Kantz, and T. Schreiber. Practical implementation of nonlinear time series methods: The TISEAN package. CHAOS 9: 413 (1999).

For further information, please write to the TISEAN group.