from PhysioNet, the research resource for complex physiologic signals


PhysioToolkit Software Index

If you use software from PhysioNet in a publication, please credit the author(s) of the software when referencing it. You can find authors' names, and in many cases their publications introducing the software, on the home pages for their contributions or in comments in the source code. If you are unsure how to cite a specific piece of software, please ask us!

Please also include the standard citation for PhysioNet:

Goldberger AL, Amaral LAN, Glass L, Hausdorff JM, Ivanov PCh, Mark RG, Mietus JE, Moody GB, Peng C-K, Stanley HE. PhysioBank, PhysioToolkit, and PhysioNet: Components of a New Research Resource for Complex Physiologic Signals. Circulation 101(23):e215-e220 [Circulation Electronic Pages; http://circ.ahajournals.org/cgi/content/full/101/23/e215]; 2000 (June 13).

First-time visitors should read An Introduction to PhysioToolkit before downloading software from this collection.

How to use this index

Look through the list of software categories below and click on any link to view a list of software in that category. Click on the Package link for any of the software to get instructions for downloading and installing it. (Our web service applications don't have package links, because there is nothing that needs to be downloaded; just click on the name of the application to run it in your web browser. The sources for these applications, which might be of interest to those running their own web servers, are available here.)

Data visualization
PhysioBank data visualization
View signals and annotations from PhysioBank and compatible data files
General-purpose data visualization
Plot text or binary data, functions, and images
Data mining
PhysioBank data mining
Collect, index, and search for essential characteristics of PhysioBank and compatible data files
Importing and exporting data
Format converters
Import and export physiologic data in text and a variety of binary formats
Creating PhysioBank-compatible recordings
Prepare and annotate your own data
Deidentification (Anonymization)
Deidentification (Anonymization)
Remove protected health information (PHI) from data to be shared
Signal and time series analysis
Physiologic signal processing
QRS and BP pulse detectors, ECG-derived respiration, apnea detection
General signal processing
Linear and nonlinear filters, signal averaging, etc.
Frequency-domain analysis of time series
Fourier and other algorithms for power spectral density estimation
Nonlinear analysis of time series
Detrended fluctuation analysis, multiscale entropy, and other methods
RR intervals, heart rate, and HRV analysis
Calculate RR intervals, NN intervals, instantaneous heart rate, heart rate variability, ectopic beat dynamics
Models
Physiologic models and simulations
Synthesize cardiovascular system variables and ECGs
Software development
Libraries and software development tools
Use these subroutines in your own software, when you need to read or write PhysioBank-compatible signal and annotation files
Development and evaluation of ECG analyzers
Test arrhythmia and ST change detection algorithms using PhysioBank and compatible data and standard software for measuring analysis algorithm performance
Other
Miscellaneous software
Build shell scripts (batch files) using these mini-applications
 
 
 
PhysioBank data visualization
Software Package Class Description Documentation Requires
WAVE WFDB 1 Analyze, view, and edit PhysioBank (and compatible) data man page
WAVE User's Guide
XView
pschart WFDB 1 Produce annotated `chart recordings' man page
PostScript printer or interpreter
psfd WFDB 1 Produce annotated `full-disclosure' (compact) plots man page
PostScript printer or interpreter
PhysioBank ATM 1 Show PhysioBank data in a web browser PhysioBank ATM a graphical web browser
SEMIA SEMIA 2 View time series of diagnostic and morphologic parameters of the Long-Term ST Database, together with the corresponding ECG waveforms and their annotations SEMIA home page;
Long-Term ST Database
WFDB, XView
rddata.m rddata.m 3 View PhysioBank signals and annotations in a Matlab figure rddata.m Matlab
 
 
 
General-purpose data visualization
Software Package Class Description Documentation Requires
plt plt 1 Make 2-D plots from text or binary data plt home page; man page
pltf plt 1 Make function plots using GNU bc and plt man page GNU bc
imageplt plt 1 plot a greyscale image using plt man page
lwcat plt 1 Postprocess plt output to make PostScript, EPS, PDF, or PNG man page
plot2d, plot3d WFDB 1 Make 2-D or 3-D plots from text data, using gnuplot man page gnuplot
 
 
 
PhysioBank data mining
Software Package Class Description Documentation Requires
pbindex pbindex 1 Collect and index essential data from PhysioBank-compatible records pbindex home page
PhysioBank Index
WFDB
pbsqsd, pbsqs pbsearch 1 PhysioBank Simple Query Server (and stand-alone command-line search tool) pbsearch home page WFDB
pbsqsc pbsearch 1 Command-line client for searching the PhysioBank Index pbsearch home page Perl 5
pbsearch pbsearch 1 Web client for searching the PhysioBank Index pbsearch home page
PhysioBank Record Search
a web browser
 
 
 
Format converters
Software Package Class Description Documentation Requires
xform WFDB 1 Convert one PhysioBank-compatible format to another, optionally changing signal amplitudes and sampling frequencies man page
a2m, ad2m, ahaconvert, m2a, md2a WFDB 1 Convert between PhysioBank-compatible formats and AHA Database formats man page
ann2rr, rr2ann WFDB 1 Convert between PhysioBank-compatible annotation files and annotation interval lists man page
RR Intervals, Heart Rate, and HRV Howto
edf2mit, mit2edf WFDB 1 Convert between PhysioBank-compatible formats and European Data Format (EDF) man page
wav2mit, mit2wav WFDB 1 Convert between PhysioBank-compatible formats and .wav audio file format man page
rdann, rdsamp, wrann, wrsamp WFDB 1 Convert between PhysioBank-compatible formats and text man pages for rdann, rdsamp, wrann, and wrsamp
PhysioBank ATM 1 Convert PhysioBank data to text, CSV, EDF, .mat, .tar.gz, or .zip formats PhysioBank ATM a web browser
 
 
 
Creating PhysioBank-compatible recordings
Software Package Class Description Documentation Requires
WAVE WFDB 1 Analyze, view, and edit PhysioBank (and compatible) data man page
WAVE User's Guide
XView
calsig WFDB 1 Calibrate signals of a PhysioBank-compatible record man page WAVE (recommended) or another signal viewer
mrgann WFDB 1 Merge PhysioBank-compatible annotation files man page
skewedit WFDB 1 Modify inter-signal skews in a PhysioBank-compatible record man page
snip WFDB 1 Copy an excerpt of a PhysioBank-compatible record man page
sortann WFDB 1 Rearrange annotations in canonical order man page
wfdbcollate WFDB 1 Collate PhysioBank-compatible records into a multi-segment record man page
record record 3 Captures data from a Philips CMS monitor record home page MS-DOS
 
 
 
Deidentification (Anonymization)
Software Package Class Description Documentation Requires
deid deid 3 Deidentify free text in medical records home page
user manual
Perl 5
edf-anonymize edf-anonymize 1 Deidentify EDF and EDF+ files man page -
 
 
 
Physiologic signal processing
Software Package Class Description Documentation Requires
sqrs, sqrs125 WFDB 1 Single-channel QRS detector based on ECG slope man page
wqrs WFDB 1 Single-channel QRS detector based on length transform man page
wabp WFDB 1 Arterial blood pressure (ABP) pulse detector man page
apdet apdet 2 Hilbert transform based sleep apnea detection using a single ECG signal apdet home page WFDB
ecgpuwave ecgpuwave 2 QRS detector and ECG waveform limit locator man page WFDB; ANSI Fortran 77 compiler (recommended: g77)
pr-comp pr-comp 1 Principal component analysis of waveforms Morphology Representation Using Principal Components WFDB
CO estimators COABP 2 Algorithms for estimating cardiac output from arterial blood pressure waveforms COABP home page Matlab
EDR edr 2 Derive a respiration signal from one or more ECG signals EDR home page; man page WFDB
puka puka 2 Detect phases of respiration in strain gauge recordings puka home page, puka manual WFDB, ecgpuwave, Matlab, Java, JMatLink, MySQL [optional], Cygwin [MS-Windows only]
TWAnalyser TWAnalyser 2 Detect and quantify T-wave alternans in the ECG TWAnalyser home page Matlab
 
 
 
General signal processing
Software Package Class Description Documentation Requires
fir WFDB 1 General-purpose FIR filter for PhysioBank-compatible records man page
mfilt WFDB 1 General-purpose median filter for PhysioBank-compatible records man page
sigamp WFDB 1 Measure signal amplitudes of a PhysioBank-compatible record man page
sigavg WFDB 1 Calculate averages of annotated waveforms man page
 
 
 
Frequency domain analysis of time series
Software Package Class Description Documentation Requires
coherence WFDB 1 Estimate the coherence and cross-spectrum of two time series of arbitrary length man page
fft WFDB 1 Estimate the power spectrum of an evenly sampled time series of arbitrary length, using a fast Fourier transform man page
lomb WFDB 1 Estimate the power spectrum of an evenly or unevenly sampled time series of arbitrary length, using the Lomb periodogram method man page
memse WFDB 1 Estimate the power spectrum of an evenly sampled time series of arbitrary length, using the maximum entropy (all-poles) method man page
 
 
 
Nonlinear analysis of time series
Software Package Class Description Documentation Requires
d3maps D3Maps 1 A visualization tool for generating animated representation of a system's dynamics D3Maps home page
dfa DFA 1 Detrended fluctuation analysis of a time series of arbitrary length DFA home page; man page
ibs IBS 2 Information-based similarity for comparison and classification of time series IBS home page
L1D2 L1D2 2 Estimate the largest Lyapunov exponent and the correlation dimension of a time series L1D2 home page
mse MSE 2 Multiscale entropy analysis MSE tutorial; man page
multifractal multifractal 3 Multifractal analysis of time series multifractal home page; A Brief Overview of Multifractal Time Series
sampen SampEn 1 Measure the sample entropy of a time series (both C and Matlab implementations are available) man page
 
 
 
RR intervals, heart rate, and HRV analysis
Software Package Class Description Documentation Requires
ann2rr, rr2ann WFDB 1 Convert between WFDB-compatible annotation files and annotation interval lists man page; RR Intervals, Heart Rate, and HRV Howto
hrfft, hrlomb, hrmem, hrplot WFDB 1 Calculate and plot heart rate time series and power spectra man page; RR Intervals, Heart Rate, and HRV Howto plt
HRV toolkitHRV 1 Visualize and filter inter-beat interval time series, and calculate time- and frequency-domain HRV statistics from them Heart Rate Variability Analysis with the HRV Toolkit plt, WFDB
ihr WFDB 1 Calculate instantaneous heart rate series from an annotation file man page; RR Intervals, Heart Rate, and HRV Howto
nguess WFDB 1 Guess the times of missing normal beats in a PhysioBank-compatible annotation file man page
pnnlist, pNNx pNNx 1 Derive pNNx statistics from an annotation interval list or an annotation file pNNx home page; man page WFDB
tach WFDB 1 Heart rate tachometer man page
activity activity 2 Estimate activity from instantaneous heart rate home page; ECG-based indices of physical activity
heartprints heartprints 1 Visualize dynamics of ventricular ectopic activity heartprints home page
 
 
 
Physiologic models and simulations
Software Package Class Description Documentation Requires
CVSim CVSim 3 Cardiovascular simulator for education and research; an elaboration of the model used in RCVSIM, with a comprehensive graphical user interface CVSim home page Java (JRE including Java Web Start required; JDK needed only to rebuild); GNU/Linux, Mac OS X (PPC or x86), or MS-Windows (not supported on other platforms)
RCVSIM RCVSIM 1 Lumped parameter model of the heart and circulation, incorporating a short-term regulatory system model and a model of resting physiologic perturbations RCVSIM home page; A Cardiovascular Simulator for Research: User's Manual and Software Guide Matlab (recommended; standalone GNU/Linux binaries are also available); WFDB
RR generators RR generators 2 Realistic RR interval time series generators from the PhysioNet / Computers in Cardiology Challenge 2002 Challenge 2002 home page
AFVP AFVP 2 Realistic generator for AA and RR intervals during atrial fibrillation AFVP home page
ECGSYN ECGSYN 2 A realistic ECG waveform generator; includes C, Java applet, and Matlab implementations ECGSYN home page; A dynamical model for generating synthetic electrocardiogram signals
ECGwaveGen ECGwaveGen 3 ECG waveform generator for Matlab or Octave ECGwaveGen home page Matlab or Octave
FECGSyn FECGSYN 2 Foetal ECG Waveform Generator FECGSyn home page Matlab or Octave
 
 
 
Libraries and software development tools
Software Package Class Description Documentation Requires
wfdb WFDB 1 Waveform Database library for C and C++ WFDB home page; WFDB Programmer's Guide; man page ANSI/ISO C compiler (recommended: gcc); optional: either libcurl (preferred) or libwww
wfdbf WFDB 1 WFDB library wrappers for Fortran man page ANSI Fortran 77 compiler (recommended: g77)
wfdb-swig wfdb-swig 3 WFDB library wrappers for Java, Perl, Python, and other languages home page WFDB, SWIG; and at least one of: Sun's Java development kit, Perl 5, Python, or another language supported by SWIG
WFDB Toolkit for Matlab wfdb-swig-matlab 1 WFDB applications implemented as Matlab functions home page Matlab 7 (R14, 2004) or later, Sun Java Runtime Environment 1.5 or later
 
 
 
Evaluation of ECG analyzers
Software Package Class Description Documentation Requires
bxb, ecgeval, epicmp, mxm, plotstm, rxr, sumstats WFDB 1 ANSI/AAMI EC-38 and EC-57 standard performance measuring software Evaluating ECG Analyzers; man pages for bxb, ecgeval, epicmp, mxm, plotstm, rxr, and sumstats
nst WFDB 1 Noise stress test for ECG analysis programs man page; Evaluating ECG Analyzers; MIT-BIH Noise Stress Test Database
EVAL_ST EVAL_ST 2 Evaluate ST episode analyzers README lesstif or Motif
 
 
 
Miscellaneous software
Software Package Class Description Documentation Requires
log10 WFDB 1 Log-transform two-column data man page
sampfreq WFDB 1 Show sampling frequency for a record man page
setwfdb, cshsetwfdb WFDB 1 Set WFDB environment variables man page
sumann WFDB 1 Summarize the contents of an annotation file man page
time2sec WFDB 1 Convert HH:MM:SS time to seconds man page
wfdb-config WFDB 1 Print WFDB library version and configuration information man page
wfdbcat WFDB 1 Copy WFDB files to standard output man page
wfdbdesc WFDB 1 Summarize the contents of a PhysioBank-compatible record man page
wfdbwhich WFDB 1 Find a WFDB file and print its pathname or URL man page
rs-toolbox Random Search Toolbox 1 A toolbox for selecting model hyper-parameters via random search. man page

About software classes

As for PhysioBank data, we describe the software available here in terms of three classes:

We make class 2 and class 3 software available via PhysioNet as a service to the research community. Contributed code is placed in classes 2 and 3 on acceptance, and may be admitted to class 1 after review and a public comment period.

About other required software

The column headed "Requires" in the software listing indicates prerequisites for each package. In a very few cases, these may indicate specific platforms, but almost all of the software available here is portable across all popular platforms, including GNU/Linux, Mac OS X, MS-Windows, and all versions of Unix.

All software is provided in source form, and since most of it is written in the C programming language, you will need a C compiler for your platform in order to compile the sources. We use and recommend gcc (a free, high quality C compiler that runs on a vast number of platforms, including all of the popular ones). Under MS-Windows, we recommend the free Cygwin development environment, which includes gcc as well as a comprehensive set of Unix-compatible development tools.

PhysioNet web service applications, such as the PhysioBank ATM, are compatible with any modern browser. We use and recommend Firefox and Chrome, and test with Lynx, Safari, and recent versions of Internet Explorer.

The WFDB software package includes many HTTP client applications that read signals and annotations directly from PhysioNet web servers without the use of a web browser. You can add this capability to your own C, C++, Fortran, and Matlab applications by linking them with the WFDB library (which provides HTTP client support via the World Wide Web Consortium's libwww library, available here).

Some of our graphical software requires the XView or LessTif toolkits. These are freely available libraries of GUI components for X Window System (X11) clients. You will also need to have an X11 server in order run X11 clients. X11 servers, XView, and LessTif are all freely available for all of the popular platforms, including GNU/Linux, Mac OS X, MS-Windows, and Unix. (For MS-Windows users, XView is available here, and LessTif and an excellent free X11 server are available as optional Cygwin packages.)

Some software requires Matlab, a popular commercial program that provides an interactive environment for numeric computation and graphics using an interpreted programming language that optionally can be compiled. Most software that requires Matlab can also be used with Octave, a freely available open-source program that is compatible with Matlab. Both Octave and Matlab can run under most popular operating systems, including GNU/Linux, Mac OS X, many versions of Unix, and MS-Windows. Sources for Octave are available here and from the official Octave web site.

Other free software

Open-source software useful for the study of physiologic signals and time series is available from other sources. Information about several such software packages is available here.