WFDB Toolbox for MATLAB and Octave

Current release: version 0.9.9
Last updated February 1, 2015 (see the change log)
[screenshot of wfdbRecordViewer]

The WFDB Toolbox for MATLAB and Octave is a collection of functions for reading, writing, and processing physiologic signals and time series in the formats used by PhysioBank databases (among others). The Toolbox is compatible with 64-bit MATLAB and GNU Octave on GNU/Linux, Mac OS X, and MS-Windows.

When using any of these functions in your work, please look at the help for that function to see how to cite the original publication and authors.

In addition, please cite the following references in any publication that make use of this toolbox:

Silva, I, Moody, G. "An Open-source Toolbox for Analysing and Processing PhysioNet Databases in MATLAB and Octave." Journal of Open Research Software 2(1):e27 [] ; 2014 (September 24).
Goldberger AL, Amaral LAN, Glass L, Hausdorff JM, Ivanov PCh, Mark RG, Mietus JE, Moody GB, Peng CK, Stanley HE. "PhysioBank, PhysioToolkit, and PhysioNet: Components of a New Research Resource for Complex Physiologic Signals." Circulation 101(23):e215-e220 []; 2000 (June 13). PMID: 10851218; doi: 10.1161/01.CIR.101.23.e215

For questions, see the FAQ; if your question is not answered there, or for contributions and feedback, please post at our community forum:!forum/wfdb-app-toolbox

The WFDB Toolbox for MATLAB and Octave is a set of Java and m-code wrapper functions, which make system calls to WFDB Software Package and other PhysioToolkit applications.

Using the WFDB Toolbox, MATLAB and Octave users have access to over 50 PhysioBank databases (over 3 TB of physiologic signals including ECG, EEG, EMG, fetal ECG, PLETH (PPG), ABP, respiration, and more). Additionally, most of these databases are also accompanied by metadata such as expert annotations of physiologically relevant events in WFDB annotation files. These can include, for example, cardiologists' beat and rhythm annotations of ECGs, or sleep experts' hypnograms (sleep stage annotations) of polysomnograms. All of these physiologic signals and annotations can be read on demand from the PhysioNet web server and its mirrors using the toolbox functions, or from local copies if you choose to download them. This feature allows your code to analyze the wide range of physiologic signals available from PhysioBank without the need to download entire records and to store them locally.

The Toolbox is open-source (distributed under the GPL), and the project's repository is located here. To simplify installation, the toolbox is distributed with precompiled native executables used by some of its functions. Sources for all of the native executables used in this toolbox can be obtained from PhysioNet (see the individual help files).

Quick Start


The WFDB Toolbox for MATLAB includes and uses its own copies of the compiled WFDB library and many of the WFDB applications. This means that separate shared libraries and executable applications are components of the toolbox for each supported platform (operating system and CPU). Installing the WFDB Toolbox for MATLAB does not interfere with any separate installation of the WFDB Software Package.

To install or update a previous installation of this Toolbox:

  1. Open MATLAB or Octave.
  2. Go into the directory where you wish to install the Toolbox:
    cd directoryname
  3. Type (or copy and paste) the following commands into the MATLAB or Octave window:
    [old_path]=which('rdsamp');if(~isempty(old_path)) rmpath(old_path(1:end-8)); end
    [filestr,status] = urlwrite(wfdb_url,'');%Octave users may have to download manually
    cd wfdb-app-toolbox-0-9-9;cd mcode

Test the Toolbox:

For a demonstration of the toolbox, run


To read and plot an ECG signal from one of PhysioBank's data collections, try these commands:


If these tests do not run successfully, please see the Toolbox FAQ for troubleshooting hints.

Toolbox functions

The toolbox's wrapper functions provide MATLAB and Octave interfaces to some of the most useful stand-alone (command-line) WFDB applications, which are more fully documented here. Many, but not all, of the features of the stand-alone applications are accessible via toolbox wrappers that have the same names as the stand-alone applications; use MATLAB's or Octave's help function to discover which features are available and how to use them. The toolbox's wfdbexec.html allows access to all features of any of the installed WFDB stand-alone applications, including any that are inaccessible via the other wrappers.

Click on the name of any of the toolbox functions in the list below to view its help file (also visible within MATLAB or Octave using the standard help function), or on the adjacent [source] link to view its source m-code.

ann2rr [source] Extract a list of intervals from an annotation file
bxb [source] ANSI/AAMI-standard beat-by-beat annotation comparator
dfa [source] Detrended Fluctuation Analysis
corrint [source] Correlation Integral Analysis
ecgpuwave [source] Estimation of QRS and P waves from ECG signals
edr [source] Derives a respiration signal from an ECG signal
gqrs [source] Estimation of QRS from ECG signals
lomb [source] Estimates power spectrum using the Lomb periodogram method
mat2wfdb [source] Writes a MATLAB variable into a WDFB record file
mrgann [source] Merge annotation files
msentropy [source] Multi scale entropy estimation
pbsearch [source] Search PhysioBank from MALTAB's browser for records with specific features
physionetdb [source] Get information about all of PhysioNet's available databases and signals
rdann [source] Read annotation files for WFDB records
rdmat [source] Read signal stored in a MAT file, converting it to physical units.
rdmimic2wave [source] Searches MIMIC II matched waveform records within a clinical time range
rdsamp [source] Read signal files of WFDB records
sortann [source] Rearrange annotations in canonical order
sqrs [source] Finds the QRS complexes of a WFDB ECG record signal
sumann [source] Summarize the contents of a WFDB annotation file
surrogate [source] Generates amplitude adjusted phase shuffled surrogate time series
tach [source] Calculates instantaneous heart rate of a WFDB ECG record signal
visgraph [source] Visibility Graph Analysis
wabp [source] Arterial blood pressure (ABP) pulse detector
wfdb [source] Prints this help information of the Toolbox
wfdb2mat [source] Converts a *.dat record file into a MATLAB *.mat file.
wfdbexec [source] Executes a system call to any installed native WFDB command.
wfdbdemo [source] Demonstration of the WFDB App Toolbox
wfdbdesc [source] Return signal information for about a WFDB record
wfdbloadlib [source] Loads WFDB Library and returns toolbox version and configuration.
wfdbRecordViewer [source] GUI for visualizing and analyzing WFDB records and annotations.
wfdbtest [source] Tests installation of the Toolbox
wfdbtime [source] Converts sample index to WFDB Time based on WFDB record information
woody [source] Performs Woody average (averaging with alignment)
wqrs [source] Finds the QRS complexes of a WFDB ECG record signal
wrann [source] Writes annotations for WFDB records into annotation files
wrsamp [source] Writes signal data into WFDB-compatible records

Frequently Asked Questions

Please make sure you check our list of frequently asked questions before contacting us! For the list of frequently asked questions, see our FAQ.


The current WFDB Toolbox for MATLAB and Octave (also known as the WFDB App Toolbox) was created by Ikaro Silva in 2012. The previous WFDB-SWIG Toolbox for MATLAB was created by Michael Craig in 2009. Original contributors of open source native code that is available at PhysioNet are credited in their respective MATLAB wrappers. In addition, the following people contributed to the development or testing of the MATLAB wrappers and the JVM interface:

Sahar Alkhairy
Fernando Andreotti
Joachim Behar
Eudald Bogatell
Gari D. Clifford
Michael Craig
Mohammad Ghassemi
Li-wei Lehman
Sara Mariani
Louis Mayaud
Bla┼ż Merela
Benjamin Moody
George Moody
Alistair E. W. Johnson
Shamin Nemati
Erina Katsumata
Daniel J. Scott
Ikaro Silva
Gabriel Squillace
Bryan Tripp

Previous Releases

Previous releases of the WFDB Toolbox for MATLAB and Octave can be found here.

Community Forum

Questions and Comments

If you would like help understanding the content of this page, or using and downloading data/software, please see our Frequently Asked Questions.

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Updated Wednesday, 19 October 2016 at 14:54 EDT

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.