All Software

• A Cardiovascular Simulator for Research: We introduce here the Research CardioVascular SIMulator ( _RCVSIM_ ) software in order to complement research with the experimental data sets provided by PhysioBank. The human cardiovascular model up…
• AFVP - A Realistic Ventricular Rhythm Model During AF: AFVP generates a synthesized beat-to-beat interval sequence of ventricular excitations with a realistic structure observed during AF.
• Apnea Detection from the ECG: Hilbert Transform based Sleep Apnea Detection using a Single Lead Electrocardiogram.
• A practical method for calculating Lyapunov exponents from small data sets: Detecting the presence of chaos in a dynamical system is an important problem that is solved by measuring the largest Lyapunov exponent. Lyapunov exponents quantify the exponential divergence of init…
• Cardiac Output Estimation from Arterial Blood Pressure Waveforms: This project contains the code used for a study that rigorously compares 11 estimates against thermodilution cardiac output (TCO) using 120 subjects from the MIMIC II database (all subjects for whom …
• Cerebral Haemodynamic Autoregulatory Information System GUI: Acute Brain injury (ABI) is a devastating event requiring intensive acute treatment and post-injury rehabilitation, both delivered for indeterminate periods of time. For severe ABIs, acute treatment …
• Code for generating the HAIM multimodal dataset of MIMIC-IV clinical data and x-rays: Code for generating the HAIM multimodal dataset of MIMIC-IV clinical data and x-rays
• CVSim: CVSim is a lumped-parameter model of the human cardiovascular system that has been developed and used for research and for teaching quantitative physiology courses at MIT and Harvard Medical School s…
• Data Chromatix: Analysis of biomedical time series plays a key role in clinical management and basic investigation. However, most conventional monitors streaming data in real-time show only the most recent values, n…
• De-Identification Software Package: The `deid` software package includes code and dictionaries for automated location and removal of protected health information (PHI) in free text from medical records.
• Detrended Fluctuation Analysis: The method of detrended fluctuation analysis has proven useful in revealing the extent of long-range correlations in time series.
• Dynamical Density Delay Maps: This project contains Matlab functions for visualizing the behavior of complex systems by means of the [ dynamical density delay mapping ("D3-Map") technique ](http://www.biomedcentral.com/content/pd…
• ECG-Derived Respiration: The ECG-Derived Respiration (EDR) technique is an approach to obtain a respiration signal from an ECG.. It is based on the observation that the positions of ECG electrodes on the chest surface move r…
• ECG-Kit: This toolbox is a collection of Matlab tools that Mariano Llamedo Soria used, adapted or developed during his PhD and post-doc work with the Besicos group at University of Zaragoza, Spain and at the …
• ECGPUWAVE: ecgpuwave analyses an ECG signal from the specified record, detecting the QRS complexes and locating the beginning, peak, and end of the P, QRS, and ST-T waveforms. The output of ecgpuwave is written…
• ECGSYN - A realistic ECG waveform generator: ECGSYN generates a synthesized ECG signal with user-settable mean heart rate, number of beats, sampling frequency, waveform morphology (P, Q, R, S, and T timing, amplitude,and duration), standard dev…
• ECG waveform generator for Matlab/Octave: ECGwaveGen generates a synthesized ECG signal with user-settable heart rate, signal duration, sampling frequency, QRS amplitude and duration, and T-wave amplitude; it uses QRSpulse to create prematur…
• edf-anonymize: _edf-anonymize_ reads an EDF or EDF+ file ( _input_ ), writing an anonymized copy of it as _output_.
• Estimating Activity from Instantaneous Heart Rate: Using only a heart rate time series, it is possible to measure a number of features that reflect the level of physical activity. Here we provide software for deriving an "activity index" based on mea…
• EVAL_ST Tool: The EVAL_ST tool is an open source tool to evaluate and compare performance and robustness of ST episode detection algorithms. The tool supports all standard and other relevant performance measures, …
• FECGSYN Toolbox: The _FECGSYN_ toolbox is a reference open-source platform for NI-FECG research, product of a collaboration between the Department of Engineering Science, University of Oxford (DES-OX), the Institute …
• 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. It repres…
• Gradient Algorithm: In finding an optimal stimulus waveform for inducing switches in neuronal states, analytical techniques from optimal control theory are often found to be difficult to use or extremely time intensive.…
• Heartprints - A Dynamical Portrait of Cardiac Arrhythmia: As part of an effort to visualize and to understand the dynamics of cardiac arrhythmias with frequent ventricular ectopy, we have developed a new representational technique termed "heartprints." Thes…
• Heart Vector Origin Point Detection and Time-Coherent Median Beat Construction: The algorithm finds the heart vector origin point and constructs the time-coherent median beat. VCG origin point is defined as the electrically quiet or isoelectric state of the heart when the heart vector does not move in 3D space.
• Information-Based Similarity: IBS is a novel method for comparing time series based on linguistic analysis of "word" frequency and rank order statistics. It has been applied successfully in a variety of applications, including an…
• Lightweight 12-lead ECG viewer for MATLAB: Clinical Viewer of raw digital 12-lead ECG file (ECG file in .txt format).
• Logistic Regression-HSMM-based Heart Sound Segmentation: Heart sound segmentation code, based on a duration-dependent hidden Markov model, extended with the use of logistic regression for emission probability estimation and an enhanced Viterbi algorithm.
• Measurement of Global Electrical Heterogeneity: The Global Electrical Heterogeneity (GEH) concept is based on the theory of Wilson's electrical gradient vector, which characterizes the degree of heterogeneity of the total recovery time across the …
• Model for Simulating ECG and PPG Signals with Arrhythmia Episodes: A model is capable of simulating sinus rhythm, atrial fibrillation and ectopic beats in ECGs and PPGs as well as extreme bradycardia and ventricular tachycardia in PPGs. Different types of noises and artifacts can also be added to the waveforms.
• 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.
• Multiscale Multifractal Analysis: Multiscale multifractal analysis (MMA) (Gierałtowski et al., 2012) is a time series analysis method, designed to describe scaling properties of fluctuations within the signal analyzed. The main resul…
• Multiscale Poincare Plots: Poincare delay maps are widely used in the analysis of cardiac interbeat interval (RR) dynamics. To facilitate visualization of the structure of these complex time series, we introduced a methodology…
• PhysioNet Cardiovascular Signal Toolbox: The PhysioNet Cardiovascular Signal Toolbox is an open-source modular program for calculating heart rate variability (HRV) implemented in Matlab with evidence-based algorithms and output formats. The…
• PhysioTag: An Open-Source Platform for Collaborative Annotation of Physiological Waveforms: Platform for collaborative and interactive annotation of physiological waveform data.
• plt - Software for 2D Plots: `plt` is a non-interactive plotting utility originally written for Unix by Paul Albrecht. `plt` can produce publication-quality 2D plots in PostScript from easily-produced text or binary data files, …
• pNNx - Time Domain Heart Rate Variability Analysis: The pNNx software package expands the analysis capabilities of the widely used pNN50 measure, providing researchers with the flexibility to test various thresholds for optimal discrimination of HRV i…
• Puka - Software for Detection of Breaths in Strain Gauge Recordings: Puka calculates descriptive statistics such as heart rate variability (HRV), peak-valley respiratory sinus arrhythmia (RSA), and respiratory variables from EKG and strain gauge respiration data.
• Random Search Toolbox: A major issue with many signal processing and machine learning algorithms is the lack of optimisation methods for determining the numerous hyper-parameters associated with the model as well as the kn…
• R-DECO: An open-source Matlab based graphical user interface for the detection and correction of R-peaks: An open-source Matlab based graphical user interface for the detection and correction of R-peaks.
• record - An application for capturing data from an HP CMS (Merlin) monitor: record is an MS-DOS application that determines what signals and measurements are available from a Hewlett-Packard (Agilent/Philips) Merlin (a.k.a. CMS or Component Monitoring System) patient monitor…
• Sample Entropy Estimation: Sample Entropy is a useful tool for investigating the dynamics of heart rate and other time series. Sample Entropy is the negative natural logarithm of an estimate of the conditional probability that…
• SEMIA: SEMIA, version 3.0.1, is a tool for viewing time series of diagnostic and morphology parameters of long-term ambulatory recordings, and ST segment annotations with their corresponding ECG waveforms o…
• Software for Analysis of Multifractal Time Series: Software for calculating multifractal partitions and moments of a time series.
• Software for computing Heart Rate Fragmentation: Heart rate fragmentation: a new method for the analysis of cardiac interbeat interval time series. The code provided can be run in Windows, Mac and Linux machines.
• 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.
• Transformer-DeID: Deidentification of free-text clinical notes with transformers: Fine tune transformer-based neural networks to deidentify clinical text data.
• TWAnalyser - A T-wave Alternans Detector: This software suite consists of Matlab implementations of the widely used Spectral Method (SM) and Modified Moving Average (MMA) for T-wave alternans (TWA) detection. It was initially developed for t…
• Waveform Database Software Package (WFDB) for MATLAB and Octave: Tools for working with waveforms in MATLAB.
• Waveform Database Software Package (WFDB) for Python: Tools for working with waveforms in Python.
• WFDB Software Package: The original Waveform Database Software (WFDB) Package, in C.
• WFDB SWIG: The wfdb-swig package provides interfaces between the WFDB library and software written in a variety of other languages, so that such software can have access to the full range of capabilities suppor…
• WFDB SWIG Toolbox for MATLAB: The WFDB SWIG Toolbox for MATLAB is a collection of applications for reading, writing, manipulating, and plotting PhysioBank data, implemented as functions in MATLAB.