Other Resources

The resources listed on this page may be of particular interest to many PhysioNet visitors. Please follow the links below to visit any of them. Links will open in another tab or window.

Additions and corrections are welcome; please send them to the address at the bottom of this page.

Featured Resources

NIH 32000 CT Images (https://nihcc.box.com/v/DeepLesion)

The National Institutes of Health’s Clinical Center has made a large-scale dataset of CT images publicly available to help the scientific community improve detection accuracy of lesions. While most publicly available medical image datasets have less than a thousand lesions, this dataset, named DeepLesion, has over 32,000 annotated lesions identified on CT images. The descriptive publication can be found at https://doi.org/10.1117/1.JMI.5.3.036501.

National Sleep Research Resource (sleepdata.org)

The National Sleep Research Resource (NSRR) offers free web access to large collections of de-identified physiological signals and clinical data elements collected in well-characterized research cohorts and clinical trials. Users can query and search across thousands of data elements, identify those data of most relevance for given needs, explore the statistical distributions of each, and download the data. Physiologic signals from overnight sleep studies are available as downloadable EDF (European data format) polysomnograms (PSGs). Users can also download standard (Rechtschaffen and Kales or AASM) annotations of these PSGs, and summary measures derived from them. The first data set available includes over 8,000 studies from exams 1 and 2 from the Sleep Heart Health Study, with scheduled new data releases every quarter from additional data sets. NSRR also provides open-source software for viewing and analyzing these data.

CI2000 (www.bci2000.org)

BCI2000 is a general-purpose system for brain-computer interface (BCI) research. It can also be used for data acquisition, stimulus presentation, and brain monitoring applications. The mission of the BCI2000 project is to facilitate research and applications in these areas. The vision for the project is that BCI2000 will become a widely used software tool for diverse areas of real-time biosignal processing. BCI2000 supports a variety of data acquisition systems, brain signals, and study/feedback paradigms, data storage in BCI2000 native or GDF formats, and data import in Matlab and export into ASCII.

Development of BCI2000 is funded by NIH/NIBIB (R01-EB006356). The system is available for free for non-profit research and educational purposes at www.bci2000.org. To date, it has been acquired by about 400 laboratories around the world, and has been used in more than 120 peer-reviewed publications.

The Open-Source Electrophysiological Toolbox (oset.ir)

OSET is a collection of electrophysiological data and open source software for biosignal generation, modeling, processing, and filtering. The toolbox is distributed under the GNU General Public License and may be freely used or modified under the specified terms of use. The software has been developed mainly in Matlab and partially in C++, but translations to other languages are welcome.

OSET has contributed data to the PhysioNet/CinC Challenge 2013. Its contributors include researchers from Shiraz University (Shiraz, Iran), Sharif University of Technology (Tehran, Iran), the Institut Polytechnique de Grenoble (Grenoble, France), and the National Aerospace University (Kharkov, Ukraine).

Biomedical Technology Research Centers: Informatics Resources

PhysioNet was established in 1999 as one of nine Biomedical Technology Resources in Simulation and Computation supported by the NIH's former National Center for Research Resources (NCRR). In October 2008, NCRR changed the name of its Biomedical Technology Research Resources (grant mechanism P41) to Biomedical Technology Research Centers, and designated the former Resources in Simulation and Computation as Informatics Resources. The NCRR was dissolved at the end of 2011; most of the resources it had funded, including PhysioNet, were transferred over a period of several years to other institutes of the NIH. Those resources include:

• Center for Integrative Biomedical Computing (formerly the Center for Bioelectric Field Modeling, Simulation and Visualization)
  University of Utah, Salt Lake City
• National Resource for Biomedical Supercomputing (High-Performance Computing for Biomedical Research)
  Carnegie-Mellon University
• The S.A.G.E. Project (formerly the Human Genetic Analysis Resource)
  Case Western Reserve University
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• Laboratory of Neuro Imaging (LONI)
  Keck School of Medicine of USC
• Multiscale Modeling Tools in Structural Biology
  Scripps Research Institute
• National Biomedical Computation Resource
  San Diego Supercomputer Center, University of California, San Diego
• VCell - The Virtual Cell (formerly the National Resource for Cell Analysis and Modeling)
  Center for Biomedical Imaging Technology, University of Connecticut Health Center
• Neuroimage Analysis Center
  Surgical Planning Laboratory, Brigham and Women's Hospital, Boston
• Resource for Biocomputing, Visualization, and Informatics (RBVI)
  Computer Graphics Laboratory, University of California, San Francisco
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• Resource for Macromolecular Modeling and Bioinformatics
  University of Illinois, Urbana-Champaign

Related Research Resources

Most of the resources listed below were also created under the aegis of the NCRR:

• Biomedical Simulations Resource (BMSR)
  University of Southern California
• Center for Computer Integrated Systems for Microscopy and Manipulation (CISMM)
  University of North Carolina
• Library of Mathematical Models of Biological Systems
  Purdue University
• National Simulation Resource (Physiome)
  University of Washington
• Yeast Resource Center
  University of Washington
• Resource Facility for Population Kinetics
  University of Washington
• Simbios: NIH Center for Biomedical Computation at Stanford (formerly the National Center for Physics-based Simulation of Biological Structures)
  Stanford University
  [Simbios encompasses SimTk and Simbiome]

Other Non-Commercial Resources

PhysioNet maintains lists of other data and software resources likely to be of interest to PhysioNet visitors, which can be found by following the links below. These lists are limited to non-commercial sites that provide access unavailable elsewhere to collections of physiologic signals or open-source software for study of physiologic signals. If you know of other resources that fit these criteria, please let us know about them.

• The open-source software listed here includes a variety of packages not currently available in PhysioToolkit, including software for nonlinear time series analysis, a complete ECG analysis application, and more.
• Collections of physiologic signals are also available from a few other sources. Among the best-known of these are the AHA and CSE databases of ECGs. Information about these databases and others is available here.