If you use resources from PhysioNet in a publication, please credit the author(s) using the citation displayed at the top of the published content. 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/content/101/23/e215.full]; 2000 (June 13).
To search content on PhysioNet, visit our search index. Databases hosted on PhysioNet include:
Electronic Health Record (EHR)
- MIMIC-III, a large, single-center database comprising information relating to patients admitted to critical care units at a large tertiary care hospital.
- The eICU Collaborative Research Database, populated with data from >200 critical care units throughout the continental United States. The data covers >160,000 patients who were admitted to critical care units in 2014 and 2015.
- MIT-BIH Arrhythmia Database, a collection of 48 fully annotated half-hour two-lead ECGs available in its entirety.
- Long-Term ST Database, a database of 86 records of ~20 hours, contains 2 or 3 ECG signals, annotated beat-by-beat and with respect to ST episodes, rhythm changes, and signal quality changes. Each record also includes ST level time series based on 16-second averages centered on each beat.
- ANSI/AAMI EC13 Test Waveforms. These 10 short recordings are specified by the current American National Standard for testing various devices that measure heart rate.
- European ST-T Database. The creators of this database, and the European Society of Cardiology, have contributed all 90 two-hour records of this database in their entirety. The reference annotation and header files for the remaining records are also available here.
- Long-Term ST Database. The creators of this database contributed half of it to PhysioNet in 2003, and the remaining records in 2007. Each of the 86 records is 21 to 24 hours long, and contains 2 or 3 ECG signals, annotated beat-by-beat and with respect to ST episodes, rhythm changes, and signal quality changes; each record also includes ST level time series based on 16-second averages centered on each beat.
- MIT-BIH Noise Stress Test Database. Twelve half-hour ECG recordings and 3 half-hour recordings of noise typical in ambulatory ECG recordings. The ECG recordings were created by adding calibrated amounts of noise to clean ECG recordings from the MIT-BIH Arrhythmia Database.
- STAFF-III Database. The STAFF III database was acquired during 1995–96 at Charleston Area Medical Center (WV, USA) where single prolonged balloon inflation had been introduced to achieve optimal results of percutaneous transluminal coronary angiography (PTCA) procedures, replacing the typical series of brief inflations. The database consists of standard 12-lead ECG recordings from 104 patients.
- BIDMC Congestive Heart Failure Database. Long-term ECGs (about 20 hours each) from 15 subjects with severe CHF (NYHA class 3-4).
- CiPA ECG Validation Study (FDA Study 3) ECG effects of ranolazine, verapamil, lopinavir+ritonavir, chloroquine, dofetilide, diltiazem, and dofetilide+diltiazem in a small sample size clinical study. The ECGCIPA database contains multi-channel ECG recordings of 60 subjects participating in the CiPA ECG validation study.
- ECG effects of Dofetilide, Moxifloxacin, Dofetilide+Mexiletine, Dofetilide+Lidocaine and Moxifloxacin+Diltiazem in Healthy Subjects. The ECGDMMLD contains data from a randomized, double-blind, 5-period crossover clinical trial in healthy male and female subjects, 18 to 35 years of age, to compare the electrophysiological response of hERG potassium channel blocking drugs with and without the addition of late sodium or calcium channel blocking drugs.
- ECG Effects of Ranolazine, Dofetilide, Verapamil, and Quinidine in Healthy Subjects. The ECGRDVQ database contains multi-channel ECG recordings of subjects partaking in a randomized, double-blind, 5-period crossover clinical trial aimed at comparing the effects of four known QT prolonging drugs versus placebo on electrophysiological and other clinical parameters.
- ECG-ID Database. Between 2 and 20 short single-lead ECG recordings from 90 volunteers, collected to support studies of using the ECG for biometric identification.
- Post-Ictal Heart Rate Oscillations in Partial Epilepsy. Seven annotated single-lead ECG recordings, with times of seizures indicated. A study of these recordings is available here.
- QT Database. Over 100 fifteen-minute two-lead ECG recordings (many excerpted from other databases), with onset, peak, and end markers for P, QRS, T, and (where present) U waves of from 30 to 50 selected beats in each recording. A paper describing this database is available here.
- Smart Health for Assessing the Risk of Events via ECG (SHAREE) Database. 24-hour Holter recordings of 139 hypertensive patients recruited at the Centre of Hypertension of the University Hospital of Naples Federico II, Naples, Italy.
- The Non-Invasive Fetal ECG Arrhythmia Database The Non-Invasive Fetal ECG Arrhythmia Database (NIFEA DB) provides a series of fetal arrhythmias recordings (n=12) and a number of control normal rhythm recordings (n=14) performed using the non-invasive fetal electrocardiography (NI-FECG) technique.
- Abdominal and Direct Fetal ECG Database. Five-minute multichannel fetal ECG recordings, with cardiologist-verified annotations of all fetal heart beats, from five women in labor, from the Medical University of Silesia, Poland. Each record includes four signals from the maternal abdomen and a simultaneously recorded reference direct fetal ECG from the fetal scalp; all signals are sampled at 1 KHz with 16-bit resolution.
- AF Termination Challenge Database. This database has been compiled for the PhysioNet/Computers in Cardiology Challenge 2004. It consists of a learning set of 30 records and two test sets of 30 and 20 records. Each record contains a one-minute excerpt of a two-lead long-term ECG recording exhibiting either self-terminating or sustained atrial fibrillation; the challenge is to identify which records in the test set show self-terminating AF.
- Creighton University Ventricular Tachyarrhythmia Database. This database includes a preliminary set of beat annotations (all beats marked as normal) with additional annotations that indicate episodes of ventricular fibrillation/flutter.
- Intracardiac Atrial Fibrillation Database. A collection of high-resolution recordings from eight subjects in atrial fibrillation or flutter; each recording includes three surface ECG signals and five intracardiac signals, all simultaneously recorded.
- Long-Term AF Database. A set of 84 long-term (24-hour) ECG recordings of subjects with paroxysmal or sustained atrial fibrillation. Each record contains two ECG signals and two sets of annotations. The original set includes unaudited markers produced by an automated QRS detector, with manual annotations of the terminations of AF episodes with durations of at least one minute. The new set contains manually reviewed reference beat type and rhythm annotations.
- Motion Artifact Contaminated ECG Database. Short duration ECG signals are recorded from a healthy 25-year-old male performing different physical activities to study the effect of motion artifacts on ECG signals and their sparsity.
- MIT-BIH Atrial Fibrillation Database (including signal files not previously released). Signal files for 23 of the 25 ten-hour records are available, along with reference rhythm annotations and unaudited beat annotations for all 25 records.
- MIT-BIH ECG Compression Test Database. This database is unannotated.
- MIT-BIH Long-Term Database. Six lengthy two-lead ECG recordings and one three-lead ECG recording.
- MIT-BIH Malignant Ventricular Arrhythmia Database. This database contains rhythm and signal quality annotations only (no beat annotations).
- MIT-BIH Normal Sinus Rhythm Database (including signal files not previously released). Also available: recordings excluded from the MIT-BIH Normal Sinus Rhythm Database (because of the presence of occasional ectopic beats).
- MIT-BIH ST Change Database. This database includes beat annotations but currently no ST change annotations. The recordings are primarily from exercise stress tests and exhibit transient ST changes.
- MIT-BIH Supraventricular Arrhythmia Database. Seventy-eight half-hour ECG recordings chosen to supplement the examples of SV arrhythmias in the MIT-BIH Arrhythmia Database.
- Non-Invasive Fetal Electrocardiogram Database. Fifty-five recordings of maternal and maternal+fetal ECGs recorded over a 20-week period from a single subject, in EDF+ format.
- PAF Prediction Challenge Database. This database has been compiled for the PhysioNet/Computers in Cardiology Challenge 2001. It consists of 100 record sets, each including a pair of 30-minute excerpts from a long-term ECG recording. Approximately half of the subjects have PAF immediately following one of the two 30-minute excerpts; among the 50 record sets in the learning set, the PAF can be studied by referring to 5-minute "continuation records" that accompany each 30-minute record. In the 50 record sets belonging to the test set, the challenge is to identify which records immediately precede PAF.
- PTB Diagnostic ECG Database. This database of 549 high-resolution 15-lead ECGs (12 standard leads together with Frank XYZ leads) includes clinical summaries for each record. From one to five ECG records are available for each of the 294 subjects.
- St. Petersburg Institute of Cardiological Technics 12-lead Arrhythmia Database. Seventy-five half-hour recordings extracted from 32 Holter records from patients undergoing tests for coronary artery disease, with reference annotation files containing over 175,000 beat annotations in all.
- Sudden Cardiac Death Holter Database. This is a collection of long-term ECG recordings of patients who experienced sudden cardiac death during the recordings. Half-hour excerpts of these recordings are available as the MIT-BIH Malignant Ventricular Arrhythmia Database.
- T-Wave Alternans Challenge Database. This database has been compiled for the PhysioNet/Computers in Cardiology Challenge 2008. It contains 100 2-, 3-, and 12-lead ECG records sampled at 500 Hz with 16-bit resolution over a ± 32 mV range, including subjects with risk factors for sudden cardiac death as well as healthy controls and synthetic cases with calibrated amounts of T-wave alternans.
- Sleep-EDF Database. This is a collection of 61 polysomnograms (PSGs) with accompanying hypnograms (expert annotations of sleep stages) from 42 subjects in two studies.
- MGH/MF Waveform Database. This is a collection of 250 recordings of 3-lead ECGs, ABP, PAP, CVP, respiration, and airway CO2 signals from patients in critical care units; some recordings include intra-cranial, left atrial, ventricular and intra-aortic pressure waveforms.
- BIDMC PPG and Respiration Dataset This dataset contains signals and numerics extracted from the much larger MIMIC II matched waveform Database, along with manual breath annotations made from two annotators, using the impedance respiratory signal.
- CEBS Database. Combined measurement of ECG, Breathing, and Seismocardiograms Database (CEBSDB). A dataset of 60 records from 20 volunteers. Each record contains two ECGs, a respiration, and a seismocardiogram signals.
- Cerebral Haemodynamic Autoregulatory Information System. Multi-channel recordings of ECG, arterial blood pressure (ABP), and intracranial pressure (ICP) of patients diagnosed with traumatic brain injury (TBI).
- Cerebral Vasoregulation in Elderly with Stroke This database contains multimodal data from a large study investigating the effects of ischemic stroke on cerebral vasoregulation. The cross sectional study compared 60 subjects who suffered strokes, to 60 control subjects, collecting the following data for each patient across multiple days: transcranial doppler of cerebral arteries, 24-h blood pressure numerics, high resolution waveforms (ECG, blood pressure, CO2 and respiration) during various movement tasks, 24-h ECG, EMG, and accelerometer recordings, and gait pressure recordings during a walking test.
- Evoked Auditory Responses in Hearing Impaired . Contains evoked Auditory Brainstem Response (ABR) and Otoacoustic Emission (OAE) recordings in eight hearing impaired listeners, in response to tone-burst stimuli across a wide range of levels.
- A Non-EEG Dataset for Assessment of Neurological Status. contains non-EEG physiological signals collected at Quality of Life Laboratory at University of Texas at Dallas, used to infer the neurological status of 20 healthy subjects. The data collected consists of electrodermal activity, temperature, acceleration, heart rate, and arterial oxygen level.
- Preterm Infant Cardio-Respiratory Signals Database. Simultaneous ECG and respiration recordings of ten preterm infants collected from the Neonatal Intensive Care Unit (NICU) of the University of Massachusetts Memorial Healthcare.
- Physiologic Response to Changes in Posture. A collection of physiological signals (ECG and ABP) in ten healthy subjects in response to a slow tilt, a fast tilt, and a standing-up maneuver.
- Response to Valsalva Maneuver in Humans Functional metrics of autonomic control of heart rate, including baroreflex sensitivity, have been shown to be strongly associated with cardiovascular risk. A decrease in baroreflex sensitivity with aging is hypothesized to represent a contributing causal factor in the etiology of primary hypertension. To assess baroreflex function in human subjects, two complementary methods to simulate the response in heart rate elicited by the Valsalva maneuver were developed and applied to data obtained from a cohort of healthy normal volunteers.
- Stress Recognition in Automobile Drivers. Recordings from healthy volunteers driving on a predefined route including streets and highways in and around Boston; signals recorded include ECG, EMG, galvanic skin resistance, and respiration.
- Wrist PPG During Exercise This database contains wrist PPGs recorded during walking, running and bike riding. Simultaneous motion estimates are collected using both accelerometers and gyroscopes to give multiple options for the removal of motion interference from the PPG traces. A reference chest ECG is included to allow a gold-standard comparison of heart rate during exercise.
- Apnea-ECG Database. This database has been assembled for the PhysioNet/Computers in Cardiology Challenge 2000. It consists of 70 ECG recordings, each typically 8 hours long, with accompanying sleep apnea annotations obtained from study of simultaneously recorded respiration signals, which are included for 8 of the recordings.
- CAP Sleep Database. The Cyclic Alternating Pattern (CAP) is a periodic EEG activity occurring during NREM sleep, and abnormal amounts of CAP are associated with a variety of sleep-related disorders. The CAP Sleep Database is a collection of 108 polysomnographic recordings from the Sleep Disorders Center of the Ospedale Maggiore of Parma, Italy. Each record includes 3 or more EEG signals together with EOG, chin and tibial EMG, airflow, respiratory effort, SaO2, and ECG signals, and reference sleep stage and CAP annotations, This database is intended to provide a useful number of carefully annotated examples of CAP in a representative variety of pathophysiologic contexts, for development and evaluation of automated CAP analyzers, as well as to support basic studies of the dynamics of CAP.
- CTU-UHB Intrapartum Cardiotocography Database. From the Czech Technical University (CTU) in Prague and the University Hospital in Brno (UHB), this database contains 552 cardiotocography (CTG) recordings, which were carefully selected from 9164 recordings collected between 2010 and 2012 at UHB. The CTG recordings start no more than 90 minutes before actual delivery, and each is at most 90 minutes long. Each CTG contains a fetal heart rate (FHR) time series and a uterine contraction (UC) signal, each sampled at 4 Hz. Each CTG is also accompanied by maternal, delivery, and fetal clinical details.
- Fantasia Database. ECG and respiration recordings, with beat annotations from 20 young and 20 elderly subjects, all healthy, in sinus rhythm during a resting state (two hours each). Half of the recordings also include (uncalibrated) continuous noninvasive blood pressure signals.
- MIT-BIH Polysomnographic Database. Includes new annotation files with sleep stage and apnea annotations.
- Santa Fe Time Series Competition Data Set B (data extracted from the MIT-BIH Polysomnographic Database).
- Motion Artifact Contaminated fNIRS and EEG Data. This data collection, contributed to PhysioBank by Kevin Sweeney and colleagues at the National University of Ireland in Maynooth, contains examples of functional near-infrared spectroscopy (fNIRS) and electroencephalogram (EEG) recordings that have been created for evaluating artifact removal methods. In each such recording, one or two pairs of similar physiological signals have been acquired from transducers in close proximity. One signal of each pair is contaminated by motion artifact, documented in each case by simultaneously recorded outputs of 3-axis accelerometers affixed to each transducer.
- OB-1 Database. This project is developing a set of recordings of fetal scalp electrograms and uterine muscular activity, with beat-by-beat annotations of the fetal ECG, to support studies of fetal heart rate variability. One sample recording is currently available; more than additional 100 data sets have been collected and are in preparation in the OB-1 project on PhysioNetWorks. Each data set documents the in-hospital course of labor and delivery (typically several hours in length), and consists of a record containing a continuous fetal ECG signal and a simultaneously recorded UC (uterine muscular activity) signal, accompanied by maternal clinical data and newborn clinical data.
- Sleep-EDF Database [Expanded]. This is a collection of 61 polysomnograms (PSGs) with accompanying hypnograms (expert annotations of sleep stages) from 42 subjects in two studies. The first was a study of age effects on sleep in healthy subjects (20 subjects, aged 25-34, with two 20-hour PSGs from consecutive nights for 19 subjects); the second was a study of temazepam effects on sleep in 22 subjects who had mild difficulty falling asleep but were otherwise healthy (9-hour PSGs of each subject on placebo). A small subset of this dataset was previously contributed in 2002 and remains available.
- Sleep Heart Health Study Polysomnography Database. A single overnight polysomnogram from this database is available here; it includes EEG, EOG, EMG, ECG, nasal airflow and respiratory effort signals, periodic measurements of SaO2 and heart rate, annotations of sleep stages, respiratory events, EEG arousals, and more.
- St. Vincent's University Hospital / University College Dublin Sleep Apnea Database. This database contains 25 full overnight polysomnograms with simultaneous three-channel Holter ECG, from adult subjects with suspected sleep-disordered breathing.
Interbeat (RR) Interval
- CAST RR Interval Sub-Study Database, comprising beat annotation files (about 24 hours each) from 809 subjects enrolled in the Cardiac Arrhythmia Suppression Trial (CAST), a landmark NHLBI-sponsored study.
- The Spontaneous Ventricular Tachyarrhythmia Database, comprising 135 pairs of RR interval time series, recorded by implanted cardioverter defibrillators in 78 subjects.
- Congestive Heart Failure RR Interval Database. Beat annotation files (about 24 hours each) from 29 subjects with congestive heart failure (NYHA classes 1, 2, and 3).
- Exaggerated heart rate oscillations during two meditation techniques, with additional data from spontaneously and metronomically breathing controls, and from highly trained athletes. These data include times of beat occurrence only (the original ECGs are not currently available).
- MIT-BIH P-wave Annotations This database contains reference p-wave annotations for twelve signals from the MIT-BIH arrhythmia database.
- Normal Sinus Rhythm RR Interval Database. Beat annotation files (about 24 hours each) from 54 subjects in normal sinus rhythm.
Gait and Balance
- Human Balance Evaluation Database, which includes force platform recordings from 193 subjects undergoing stabilography tests.
- The Gait in Parkinson's Disease Dataset, a collection of multichannel recordings from force sensors beneath the feet of 93 patients with Parkinson's Disease and 73 healthy controls, collected over three studies.
- Gait Dynamics in Neuro-Degenerative Disease Database. A collection of 64 recordings of gait (including original foot signals) from 15 subjects with Parkinson's disease, 20 with Huntington's disease, 13 with amyotrophic lateral sclerosis, and 16 healthy controls.
- Gait in Aging and Disease Database (a "mini-collection" of data from healthy young and old volunteers, and patients with Parkinson's disease)
- Gait Maturation Database (a collection of data from healthy children ages 3-14)
- Long Term Movement Monitoring Database. 3-day 3D accelerometer recordings of 71 elder community residents, used to study gait, stability, and fall risk.
- Noise Enhancement of Sensorimotor Function. Measurements of postural sway in 27 healthy volunteers (15 young, 12 elderly), with and without subsensory stimulation of the soles of the feet using mechanical noise.
- Tai Chi, Physiological Complexity, and Healthy Aging—Gait. Two-channel gait recordings of 87 older adults from the Greater Boston area. Subjects were from a hybrid study design that included a two-arm randomized clinical trial (RCT) along with an additional observational comparison group.
- Unconstrained and Metronomic Walking Database (a collection of long-term recordings of gait dynamics from 10 healthy young volunteers).
Neuroelectric and Myoelectric
- Squid Giant Axon Membrane Potential Database, which contains single-unit neuronal recordings of squid giant axons in response to stimulus currents. The membrane potential and stimulus current are given for a total of 170 trials across 8 different axons.
- Icelandic 16-electrode EHG Database, comprising 122 electrohysterogram recorded with 16-electrodes from 45 pregnant women.
- CHB-MIT Scalp EEG Database. EEG recordings of 22 pediatric subjects with intractable seizures, monitored for up to several days following withdrawal of anti-seizure medication to characterize their seizures and assess their candidacy for surgical intervention. In all, the onsets and ends of 182 seizures are annotated.
- EEG During Mental Arithmetic Tasks The database contains EEG recordings of subjects before and during the performance of mental arithmetic tasks.
- EEG Motor Movement/Imagery Dataset. One- and two-minute recordings of 109 volunteers performing a series of motor/imagery tasks. Each record contains 64 channels of EEG recorded using the BCI2000 system, and a set of task annotations.
- EEG Signals from an RSVP Task. This project contains EEG data from 11 healthy participants upon rapid presentation of images through the Rapid Serial Visual Presentation (RSVP) protocol at speeds of 5, 6, and 10 Hz.
- Effect of Deep Brain Stimulation on Parkinsonian Tremor. Rest tremor velocity in the index finger of 16 subjects with Parkinson's disease, who receive chronic high frequency electrical deep brain stimulation.
- ERP-based Brain-Computer Interface recordings. Annotated 64-channel EEGs with 4-channel EOGs sampled at 2048 Hz from 10 subjects; 20 short records for each subject, generated while focusing on specified target characters displayed by a traditional matrix speller. This dataset was generated as part of a study aimed at identifying the factors limiting the performance of brain-computer interfaces based on event-related potentials (ERPs).
- Evoked Auditory Responses in Normals across Stimulus Level. Evoked auditory response in 8 healthy subjects across a wide range of stimulus levels, including 24-bit recordings of auditory brainstem response (ABR) and otoacoustic emission (OAE) signals, and psychoacoustic loudness estimates.
- Icelandic 16-electrode EHG Database. 122 16-electrode electrohysterogram recordings from 45 pregnant women, obtained at the Akureyri Primary Health Care Centre, Landspitali University Hospital, and Akureyri Hospital in Iceland. These include 10 recordings of women in labor, as well as 112 recordings of women in their third trimester who were not currently in labor. Each record also includes a scanned copy of the printed tocograph.
- MAMEM Steady State Visually Evoked Potential Database The MSSVEP database contains 256 channel EEG recordings of 11 subjects under the stimulation of flickering lights, used to study the steady state visually evoked potentials.
- MMG Database. Uterine magnetomyographic (MMG) signals from 25 pregnant women, recorded using the 151 channel SARA (SQUID Array for Reproductive Assessment) system installed at UAMS, Little Rock, USA.
- Squid Giant Axon Membrane Potential. The SGAMP database contains single-unit neuronal recordings of squid giant axons in response to stimulus currents. The membrane potential and stimulus current are given for a total of 170 trials across 8 different axons.
- Term-Preterm EHG Database. Electrohysterogram (EHG: uterine EMG) recordings obtained at the University Medical Centre Ljubljana from 300 pregnant women, including 262 who had full-term pregnancies and 38 whose pregnancies ended prematurely, and including 162 recordings made before the 26th week of gestation and 138 made later.
- The Term-Preterm EHG DataSet with Tocogram The Term-Preterm ElectroHysteroGram DataSet with Tocogram (TPEHGT DS) contains 26 four-signal 30-min uterine EHG records, i.e., three EHG signals accompanied by a simultaneously recorded external tocogram measuring mechanical uterine activity (TOCO signal) of pregnant women, and another five 30-min uterine records (EHG signals and TOCO signal) of non-pregnant women.
- UniCA ElectroTastegram Database (PROP). Contains 39 differential biopotential measurements recorded from the tongues of as many healthy voluntary human subjects (16 males, 23 females, equally divided into the three PROP taster status classes), during a stimulation with 30uL, 3.2 mmol/L solution of 6-n-propylthiouracil (PROP).
- Examples of Electromyograms. Short EMG recordings from three subjects (one without neuromuscular disease, one with myopathy, one with neuropathy).
- The Concept Unique Identifier (CUI)-less database (CUILESS2016), which contains a corpus of "CUI-less" concepts taken from the SemEval2015 Task 14 that have been assigned CUIs.
- Deidentified Medical Text Database, a gold standard corpus of 2,434 nursing notes that have been thoroughly deidentified, along with a set of associated annotations. Identifiers are replaced with realistic surrogate data.
- 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 command-line tools.
- 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.
- 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. 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 measurements.
- 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.
- Distributed Computing with PhysioNet data. A brief tutorial on how to cloud processing PhysioNet data with WFDB, StarCluster, Amazon EC2, Octave, and Hadoop.
Exploration and analysis
- 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 dynamics.
- 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 analysis (DFA).
- 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 rate.
- 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.
- Generalized Multiscale Entropy (GMSE) Analysis. Discusses ways to generalize the concept of MSE by using different coarse-graining functions, and illustrates the differences between these methods using both interbeat interval data and simulated data.
- 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.
- 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.
- 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 to PhysioBank.
- 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 Cookbook. 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.
- 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 paper 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 Lake City.
- 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, Dresden).
- Openeering. 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 programming.
To search content on PhysioNet, visit our search index. Software hosted on PhysioNet includes:
- PhysioBank ATM. PhysioBank’s Automated Teller Machine is a self-service facility for exploring PhysioNet databases using your web browser.
- SEMIA. SEMIA is a tool for viewing time series of diagnostic and morphology parameters of long-term ambulatory recordings.
- Multiscale Poincare Plots. Matlab software for visualizing the complexity of time series on multiple time scales.
Signal and time series (general)
- WFDB Library (C). Effective use of PhysioBank data requires specialized software. We have developed a large collection of such software over the past twenty years, and much of it is contained within the WFDB (WaveForm DataBase) Software Package.
- WFDB Library (Python). The Python WFDB Toolbox is an implementation of the WFDB in the Python programming language, enabling simple installation and reuse.
Signal and time series (complexity)
- Generalized Multiscale Entropy Analysis. The method of generalized multiscale entropy (GMSE) analysis is useful for investigating complexity in physiologic signals and other series that have correlations at multiple (time) scales.
- Transfer Entropy With Partitioning. This is a repository of MATLAB functions that can estimate transfer entropy (information flow) from one time series to another using a non-parametric partitioning algorithm.
- Sample Entropy Estimation. Sample Entropy is a useful tool for investigating the dynamics of heart rate and other time series.
- Multiscale Entropy Analysis. The method of multiscale entropy (MSE) analysis is useful for investigating complexity in physiologic signals and other series that have correlations at multiple (time) scales.
- Perl deid. The Perl deid software package includes code and dictionaries for automated location and removal of protected health information (PHI) in free text from medical records.
- EDF-anonymize. EDF-anonymize reads an EDF or EDF+ file (input), writing an anonymized copy of it as output.
- CVSim. Cardiovascular simulator for education and research; an elaboration of the model used in RCVSIM, with a comprehensive graphical user interface.
- RCVSIM. Lumped parameter model of the heart and circulation, incorporating a short-term regulatory system model and a model of resting physiologic perturbations.
- AFVP. Realistic generator for AA and RR intervals during atrial fibrillation.
- ECGSYN. A realistic ECG waveform generator; includes C, Java applet, and Matlab implementations.
- FECGSyn. Foetal ECG Waveform Generator.
- Gradient Algorithm. Applications of a stochastically-seeded gradient algorithm.
To search content on PhysioNet, visit our search index. Challenges hosted on PhysioNet include:
- 2000: Detecting Sleep Apnea from the ECG.
- 2001: Predicting Paroxysmal Atrial Fibrillation.
- 2002: RR Interval Time Series Modeling.
- 2003: Distinguishing Ischemic from Non-Ischemic ST Changes.
- 2004: Spontaneous Termination of Atrial Fibrillation.
- 2005: The First Five Challenges Revisited.
- 2006: QT Interval Measurement.
- 2007: Electrocardiographic Imaging of Myocardial Infarction.
- 2008: Detecting and Quantifying T-Wave Alternans.
- 2009: Predicting Acute Hypotensive Episodes.
- 2010: Mind the Gap.
- 2011: Improving the quality of ECGs collected using mobile phones.
- 2012: Predicting mortality of ICU patients.
- 2013: Non-invaside fetal ECG.
- 2014: Robust detection of heart beats in multimodal data.
- 2015: Reducing false arrhythmia alarms in the icu.
- 2016: Classification of Normal/Abnormal Heart Sound Recordings.
- 2017: CAF Classification from a Short Single Lead ECG Recording.
- 2018: You Snooze, You Win.