PhysioNet tutorials are intended to provide hands-on introductions to
the data and software available from this resource. This index lists
currently available PhysioNet tutorials by category, as well as reference
manuals, workshop materials, and links to other tutorials likely to be
of interest to PhysioNet visitors.
- A Brief Tour of PhysioNet. An interactive introduction
to this resource, highly recommended for first-time visitors.
- An Introduction to the
PhysioBank Archives. PhysioBank contains well over 36,000 recordings
of annotated, digitized physiologic signals and time series; this
brief tutorial begins with an exploration of these archives using
your web browser, followed by pointers on downloading data, information
about the archives themselves, and recommendations of software available
freely from this site for further study of PhysioBank data.
- An Introduction to
PhysioToolkit. PhysioNet's collection of software for
viewing, analyzing, and modelling physiologic signals and time
series consists of open-source software that can be studied,
verified, and modified to suit the specific needs of your work.
How to ...
- Finding records in PhysioBank.
This tutorial describes the PhysioBank Index of over 36,000 records that
can be viewed by the PhysioBank ATM, and how to find records with desired
characteristics using the web-based PhysioBank Record Search or via
- How to obtain PhysioBank data in text
form. Many readers wish to convert binary data from PhysioBank
(PhysioNet's data archive) into text form for further processing. There
are many good reasons
not to do so. If you are determined to do it anyway, here's how.
- Creating PhysioBank (WFDB-compatible)
Records and Data Collections. If you have digital recordings of signals
or time series, perhaps with annotations, that you would like to study using
PhysioToolkit software such as that in the WFDB software package, or that
you would like to contribute to PhysioBank, this tutorial should get you
started on creating PhysioBank-compatible records from your data.
- How to set up a mirror of
PhysioNet. A PhysioNet mirror can run on almost any computer made
in the last ten years, and it can provide local users with fast
access to PhysioBank data and PhysioToolkit software, even in areas
with slow or unreliable Internet connections. PhysioNet mirrors are
easy to set up and essentially self-maintaining. Put an old computer
to good use and help PhysioNet users in your area.
- Using the MIMIC II
Database. The MIMIC II Database
has many types of data that are not available in other PhysioBank
data collections. This tutorial is intended to help you get
started on a project that makes use of this rich data collection.
- An Introduction to Cygwin.
PhysioToolkit includes a large collection of open-source, POSIX-compliant
software that can be useful to most PhysioNet visitors. Since almost all
of the popular platforms are also POSIX-compliant, it's easy to get
PhysioToolkit software running on those platforms, including GNU/Linux,
Mac OS X, and all versions of Unix. Microsoft Windows is not
POSIX-compliant, but a free software package called Cygwin provides a
stable and very complete POSIX layer on top of Windows. By installing
Cygwin on your Windows PC, you will be able to run PhysioToolkit software
on it. This tutorial explains how to do so, without interfering with
any Windows software you may be using.
- Applying PhysioNet tools to manage neurophysiological
signals. How to import and handle data from commercial devices using
PhysioToolkit and other open source software. This tutorial was
contributed by Jesus Olivan Palacios, a neurophysiologist who has written
an excellent introduction to much of the software available from PhysioNet
in the form of a series of hands-on exercises using data provided with the
tutorial. Very readable, and highly recommended for neurophysiologists and
others alike. (Also see Sciteam, below, by the same author.)
- RR Intervals, Heart Rate, and HRV Howto. A
brief overview of how to obtain inter-beat (RR) interval and heart rate
time series, and of some basic methods for characterizing heart rate
variability, using freely available PhysioToolkit software.
- Heart Rate Variability Analysis with the
HRV Toolkit: Basic Time and Frequency Domain Measures. This
tutorial describes how to use the HRV toolkit (available here) to
select and prepare time series of inter-beat intervals and to calculate
measurements of the basic time- and frequency-domain HRV
statistics that are widely used in the literature. Particular
attention is given to techniques for identifying and dealing with
outliers, in order to permit reliable determination of
- Morphology Representation Using Principal
Components. Using the QRS complex of the ECG as an example,
this tutorial presents practical methods for principal
component analysis of waveforms, including software that can be used as
is or customized as desired.
- Evaluating ECG Analyzers. How
to use PhysioToolkit software and data available from PhysioBank and
other sources to measure the performance of a QRS detector or classifier,
in accordance with protocols prescribed by current ANSI standards and the
US FDA (ANSI/AAMI EC38 and EC57).
- Digitizing Paper ECGs and Other
Plots. A brief survey of resources that may be helpful.
- How to create and manage a
PhysioNetWorks project. The essential information needed to create,
build, and complete a PhysioNetWorks project.
- How to Write HTML pages for
PhysioNet. If you are preparing a contribution of data, software,
or tutorial material for PhysioNet, this guide illustrates how to create
pages with the templates and style sheets used on this web site.
- Distributed Computing with PhysioNet data. A brief tutorial on
how to cloud processing PhysioNet data with WFDB, StarCluster, Amazon EC2, Octave, and Hadoop.
Also see Reference Guides below, on-line books
containing a wealth of additional "how-to" information.
Exploring Data and Novel Analyses
- Variability vs. Complexity. Introduces students
and trainees to the study of complex variability, especially in
physiology and medicine.
- Exploring Patterns in Nature. A set of interactive
tutorials drawn from current research, focussing on emergent phenomena
(random behavior at the smallest scales leading to patterns at larger
scales). Subjects include fractal coastline and dimension, measuring
randomness, physical and chemical branching structures, biological
branching patterns, diffusion, percolation, and motion on a fractal.
These tutorials do not assume extensive knowledge of mathematics.
- Nonlinear Dynamics, Fractals, and Chaos Theory:
Implications for Neuroautonomic Heart Rate Control in Health and
Disease. An introduction to some key concepts of nonlinear
- Exploring Human Gait and Heart Rate Dynamics.
Use two sets of time series derived from human subjects to
study changes in dynamics with age and disease, with a variety of
methods including approximate entropy (ApEn) and detrended fluctuation
- Fractal Mechanisms in Neural Control: Human Heartbeat
and Gait Dynamics in Health and Disease. Beginning with a
definition of fractal dynamics, this tutorial explores how fractal
analysis may reveal information of diagnostic or prognostic value
when applied to two model systems.
- A Brief Overview of Multifractal Time Series.
A concise review of how fractal and multifractal patterns in time can
be quantified, including a short discussion of multifractality in heart
- Approximate Entropy (ApEn). A brief
description of how to calculate ApEn, a ``regularity statistic'' that
quantifies the unpredictability of fluctuations in a time series,
including a worked-out example.
- Multiscale Entropy (MSE) Analysis.
Introduces the concept of MSE, describes an algorithm for calculating MSE
using sample entropy (SampEn), presents a portable implementation of this
algorithm, and illustrates its application to analysis of interbeat (RR)
interval time series from PhysioBank.
- Information Based Similarity Index.
An introduction to a novel linguistic analysis method that has been
successfully applied to studies of inter-beat interval time series, the
origin of the SARS coronavirus, and the authorship of Shakespeare's plays.
Materials from these workshops include tutorial presentations and related
- Electronic Interchange of Polysomnography
Data. Presentations from a workshop to develop guidelines for PSG
transmission and archiving, including presentations on needs of
researchers, standards efforts, and existing formats for PSGs and
other physiologic signals.
- HRV 2006. Materials from our mini-course
about heart rate variability, including presentations on physiologic
mechanisms of HRV, time and frequency domain measures, complexity measures,
clinical applications, and more.
Books describing the major components of
PhysioToolkit are also available here.
Printed copies of some of these books may be purchased from
Bookstore. These books incorporate both tutorial and reference
- WFDB Programmer's Guide.
Essential material for those wishing to read (or create) PhysioBank
data files from their own software. This book includes detailed
descriptions of the application programming interfaces for digitized
signal and annotation files, and sample applications including digital
filters, signal averaging, and a QRS detector.
- WFDB Applications Guide.
How to use several dozen small tools individually and in combination to
view, manipulate, and analyze PhysioBank and similar data. This guide
includes the tutorial on evaluating ECG
analyzers mentioned above.
- WAVE User's Guide. A
comprehensive introduction to WAVE, an interactive graphical interface
- RCVSIM User's
Manual and Software Guide.
This guide introduces the Research Cardiovascular Simulator (RCVSIM),
software for synthesizing realistic human pulsatile hemodynamic waveforms,
cardiac function and venous return curves, and beat-to-beat hemodynamic
variability. The manual includes a description of the cardiovascular
models used by RCVSIM, guides to reading and compiling the RCVSIM source
code, and a tutorial with examples illustrating its use
- plt Tutorial and
This book introduces plt, a highly capable and flexible utility
for making publication-quality 2D plots from text or binary data files.
plt has a very broad range of applications, and is well-suited for
visualizing the output of many of the PhysioToolkit applications.
Other tutorial resources of interest
Tutorials listed in this section are not hosted by PhysioNet. Links
will open in a new browser window.
- ECG Wave-Maven. This is a self-assessment program on
interpretation of 12-lead diagnostic ECGs, with over 400 case studies. Use the
program to test your diagnostic abilities, or browse through the cases in
reference mode. ECG Wave-Maven was developed at Harvard Medical School
and Boston's Beth Israel Deaconess Medical Center. Its creators have written a
describing the goals and technology behind the program, and a survey of its use
during its first 17 months of operation.
- The Alan
E. Lindsay ECG Learning Center in Cyberspace. A comprehensive
introduction to clinical electrocardiography, developed at LDS Hospital, Salt
- A guided tour through TISEAN: Exercises with data sets.
This tutorial introduces a large package of software for nonlinear time series
analysis developed 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,
- Sciteam. This site offers tutorials on Scilab (an
open-source programming environment developed at INRIA for ``numerical
computations in a user-friendly environment'') and how to use it with
PhysioBank data and PhysioToolkit software. Scilab is similar to Matlab, but
offers many additional features. The tutorials are written by and for clinical
neurophysiologists, and do not assume extensive knowledge of mathematics or