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:
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
- Physionet/CinC Challenge Software Archive
- Software contributions from successful entrants of past PhysioNet/CinC challenges. The listed software has been successfully tested at least once during the year of the entry. Unless the link opens to a physiotoolkit page, the software is treated as an archive and is not supported by Physionet. Older challenges may have fewer or no contributions, but the rest of this software index page may contain relevant tools not directly contributed for the challenges.
- 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 |
|---|---|---|---|---|---|
| dchromatix | dchromatix | 2 | A simple chromatic method for visualizing trends in biomedical signals | dchromatix home page | Matlab |
| mpp | mpp | 2 | Multiscale Poincare Plots - Visualize the complexity of time series on multiple time scales | mpp home page | Matlab |
| 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 |
| CHARIS GUI | CHARIS GUI | 2 | GUI to calculate and display intracranial pressure (ICP) information. | CHARIS GUI home page | Matlab |
| 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 |
| ECG-kit | ECG-kit | 3 | Allows the use of several popular algorithms for ECG processing | ECG-kit | Matlab |
| GEH | GEH | 2 | These software scripts calculate Global Electrical Heterogeneity scores of ecg signals, which characterize the degree of heterogeneity of the total recovery time across the ventricles. | GEH Home Page | Matlab |
| PhysioNet Cardiovascular Signal Toolbox | PCST | 1 | An open-source modular program for calculating heart rate variability (HRV) implemented in Matlab with evidence-based algorithms and output formats. | PCST 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 | 2 | A visualization tool for generating animated representation of a system's dynamics | D3Maps home page | Matlab |
| dfa | DFA | 1 | Detrended fluctuation analysis of a time series of arbitrary length | DFA home page; man page | |
| gmse | GMSE | 2 | Generalized multiscale entropy analysis | GMSE tutorial | |
| 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 | |
| mma | MMA | 2 | Multiscale multifractal analysis | MMA Homepage | Matlab |
| 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 | |
| tewp | TEWP | 2 | Transfer Entropy With Partitioning | TEWP home page | Matlab |
| 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 toolkit | HRV | 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 |
| Gradient Algorithm | Gradient Algorithm | 2 | Applications of a stochastically-seeded gradient algorithm | Gradient Algorithm home page | Matlab |
| 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 |
| *Archive Software Contributions for PhysioNet/CinC Challenges | ||
| Challenge Year | Software | Challenge Description |
|---|---|---|
| 2000 | Contribution | Detecting Sleep Apnea from the ECG. |
| 2001 | None | Predicting Paroxysmal Atrial Fibrillation. |
| 2002 | Contribution | RR Interval Time Series Modeling. |
| 2003 | Contribution | Distinguishing Ischemic from Non-Ischemic ST Changes. |
| 2004 | Contribution | Spontaneous Termination of Atrial Fibrillation. |
| 2005 | None | The First Five Challenges Revisited. |
| 2006 | Contributions | QT Interval Measurement. |
| 2007 | None | Electrocardiographic Imaging of Myocardial Infarction. |
| 2008 | Contributions | Detecting and quantifying T-wave alternans. |
| 2009 | Contributions | Predicting acute hypotensive episodes. |
| 2010 | Contributions | Mind the gap. |
| 2011 | Contributions | Improving the quality of ECGs collected using mobile phones. |
| 2012 | Contributions | Predicting mortality of ICU patients. |
| 2013 | Contributions | Non-invasive fetal ECG. |
| 2014 | Contributions | Robust detection of heart beats in multimodal data. |
| 2015 | Contributions | Reducing false arrhythmia alarms in the ICU. |
| 2016 | Contributions | Classification of normal/abnormal heart sound recordings. |
| 2017 | Contributions | AF classification from a short single lead ECG recording. |
| 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. | home page | |
About software classes
As for PhysioBank data, we describe the software available here in terms of three classes:
- Class 1 (fully supported, extensively and rigorously tested software)
- Class 2 (archival copies of software that supports published research, contributed by authors, together with corrections and improvements submitted by authors and users)
- Class 3 (code not supported by PhysioNet; includes contributed code that may be supported by its authors, as well as beta-quality code that may require further development, testing, and documentation)
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.
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If you would like help understanding, using, or downloading content, please see our Frequently Asked Questions. If you have any comments, feedback, or particular questions regarding this page, please send them to the webmaster. Comments and issues can also be raised on PhysioNet's GitHub page. Updated Friday, 21-Oct-2016 22:24:23 CEST |
PhysioNet is supported by the National Institute of General Medical Sciences (NIGMS) and the National Institute of Biomedical Imaging and Bioengineering (NIBIB) under NIH grant number 2R01GM104987-09.
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