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The goal of this project is to create a survey of Publicly Available InVivo Medical Imaging Archives and the underlying software capabilities. It is generally agreed that there is a need for public medical imaging archives to provide the biomedical research community, industry, and academia with access to images that support:
The purpose of this project is to provide a practical guide for the community which allows them to:
We encourage any feedback from the wider community that may help improve this information or correct any misconceptions stated below. The survey is divided into two sections:
The following table is a list of publicly accessible DICOM based biomedical image archives. Following the table is an analysis of what was found upon reviewing each archive in August 2010.
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Supporting Institution(s) |
Cancer Imaging Program, caBIG |
NIAMS, caBIG |
WUSTL, BIRN |
Lab of NeuroImaging UCLA (LONI) |
BIRN |
BIRN |
Lung Cancer Alliance |
Optical Society of America |
NIH, NDAR |
Insight Journal |
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Content Type |
In Vivo Cancer Imaging |
Osteoarthritis |
Biomedical images and meta data |
ADNI (Alzheimers), |
Brain scans |
ELUDE (Elderly Depression), |
Patient-contributed Medical scans |
Optical |
Normal brain development |
Biomedical images and meta data |
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Archive Software |
NBIA |
XNAT |
Image Data Archive |
custom |
XNAT |
MIDAS |
MIDAS |
custom |
MIDAS |
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Login account required |
For advanced site features or limited access data sets, but is not required for accessing public data |
Yes |
For accessing limited access data sets, but not for public data |
Yes, via email address. Used only for providing links for downloading data. |
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For accessing limited access data sets, but not for public data |
No |
For accessing limited access data sets, but not for public data |
Yes |
For accessing limited access data sets, but not for public data |
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Explicit data sharing policy |
Yes, with options for uploading fully open or limited access data sets |
Yes, found here |
No |
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Accepting new data |
Yes, with approval from NCI CBIIT/CIP |
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Yes, users can register accounts and upload data |
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Central curation/review |
Yes, performed by CBIIT/CIP staff |
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No |
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Availability/Uptime |
~99%, hosted on a redundant production system at NCI CBIIT |
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Project- or Collection- based groupings? |
Yes |
Yes |
Yes |
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Yes |
Yes |
Yes |
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Yes |
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Size of Current Volume |
~3TB |
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number of DICOM Tags query-able |
~90 |
~90 |
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DICOM transfer protocol |
For submission, but not download |
For submission, but not download |
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methods to download DICOM data |
Web (zip), FTP, Java Webstart client |
Web (zip), FTP, Java Webstart client |
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Helpdesk Support |
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Affiliation with Journal |
No |
No |
No |
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NBIA
LONI homepage: http://www.loni.ucla.edu/
Image Data Archive - http://www.loni.ucla.edu/Research/Databases/
BIRN data portal: http://www.birncommunity.org/resources/data/
BIRN is connected with multiple institutions which host multiple archives using different software and containing different data sets.
http://www.insight-journal.org/midas/
A MIDAS based image archive which contains a number of data sets contributed from NAMIC, NLM, Kitware, the Insight Software Consortium, and more. "Communities" listed on the site include:
From their homepage-
*Give A Scan* is the world's first patient-powered, publicly available archive of images and clinical data on lung cancer patients. All the data has been donated by patients in order to encourage more researchers to focus on lung cancer and to accelerate progress in the early detection, diagnosis and treatment of lung cancer which is now the leading cause of cancer death worldwide.
As of August 2010 the archive contains 9 "communities" which appear to be 9 patients with lung cancer totaling approximately 1GB of data. The site provides some meta data information about the images and clinical info about the subjects. Images are hosted in DICOM format. The archive can be browsed by Community/patient/study/series or searched by modality and other image meta data.
The archive is hosted by the Kitware image archive solution called MIDAS: http://www.kitware.com/products/midas.html
http://midas.osa.org/midaspub/
This archive is a collection of optical images. Like the Lung Cancer Alliance archive it is also hosted using Kitware's MIDAS archive software. This archive hosts 6 top level "communities" which contain anywhere from 4 to 242 items within them. In this case it seems not all of the data is DICOM but some of it is. Three of the Communities appear to be unrelated demonstration collections not tied to OSA as they contain lesion sizing data sets of lung images.
http://archive.nlm.nih.gov/proj/webmirs/
WebMIRS is the National Library of Medicine's (NLM) tool used for hosting two related datasets and related spine x-ray images which are part of the National Health and Nutrition Examination Survey (NHANES). The site requires registration and login through a java web client to view the data set. Most of the data is text based, but there are spine x-rays for some of the patients. The client allows for searching but not really browsing. The user must enter a boolean search query in order to retrieve any patient results. It does not appear that it is possible to actually download the images, rather that you can only view them in the WebMIRS client.
National Alliance for Medical Image Computing (NA-MIC) Image Gallery: http://www.na-mic.org/publications/gallery
As of October 2010 this consisted of ~383 images. All images appear to be JPGs or similar compressed file types rather than actual DICOM. The purpose of this gallery seems to be to create a repository for images, charts, and figures referenced in publications submitted to NA-MIC's publication database (http://www.na-mic.org/publications). Images can be browsed by patient/study/series or searched by modality and a number of other image based features.
Part of the National Database for Autism Research (NDAR) program.
According to http://ndar.nih.gov/ndarpublicweb/aboutNDAR.go#federation-
The Pediatric MRI Data Repository will be the first in this series to be made available to ASD researchers, in the summer of 2010. At that time, investigators will be able to perform a single query in the NDAR portal to view results across multiple datasets.
The original Pediatric MRI Data Repository is located at https://nihpd.crbs.ucsd.edu/nihpd/info/index.html. Access to the data requires filling out multiple forms and faxing them to an office at NIH to receive permission. I have not yet requested access at this time to find out exactly what's in the archive, however some information about their quality control processes reveal a little about the image protocols and can be learned about here: https://nihpd.crbs.ucsd.edu/nihpd/info/quality_control.html
The NIH Image Bank is located at http://media.nih.gov/imagebank/index.aspx
According to http://media.nih.gov/imagebank/about.aspx-
The NIH Image Bank contains images from the collections of the 27 institutes and centers that comprise the National Institutes of Health. Contents include general biomedical and science-related images, clinicians, computers, patient care-related images, microscopy images, and various exterior images.
The point of the image bank appears to be more for promotional and marketing images. I did not notice any high quality medical images of actual patients or DICOM files which might be usable for research purposes.
http://www.eortc.be/services/forms/erp/default.aspx
According to their site investigators can make requests for access to data collected as part of EORTC trials after the primary end point has been published on. I did not see any place that outlined what trials are being conducted, what trials have been completed and reached their publication of primary endpoint, or exactly what types of data are collected. However in the PDF on this page which outlines their data sharing policy in more detail it lists in the section "4.3 Data Transfer" that "data will preferentially transferred in the form of an ASCII file (with .dat extension), with associated SAS programs to load the data into SAS." I saw no mention of how they handle images in this section and thus assume they may not collect or distribute any.
h2. Image archive software solutions
Below is a list of image archive solutions that can be deployed by interested parties wishing to build their own DICOM based biomedical image archive. This list omits some of the archives above in cases where we could not find any information about how one might download and deploy their own instance of the software.
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Interface/GUI |
Web |
Web |
Web |
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Query types/flexibility |
Simple (9 parameters), Advanced (10 more parameters), Dynamic (boolean query of up to 90 DICOM tags) |
Limited subset of DICOM tags out of the box but is highly configurable for adding the ability to query on just about any kind of meta data you wish to provide |
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Role Based Security |
Yes |
Yes |
Yes |
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Public access option (no login req) |
Yes |
Yes |
Yes |
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Active Development |
Yes, NCI CBIIT |
Yes, WUSTL Neuroinformatics Research Group |
Yes, Kitware |
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Supports Federated Implementation |
Yes, can discover other nodes on the caGrid |
Not currently, but there are plans to add this functionality eventually |
No |
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API available |
Yes, caGrid |
Yes, ?RESTFUL web services? |
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Supported image formats |
DICOM |
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Supported metadata formats |
XML, Zip |
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Transfer protocols (import/export) |
DICOM, HTTPS |
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Controlled Vocabulary |
caBIG |
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Deployment Support |
Yes, CBIIT Application Support or via NBIA User Listserv |
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Support Operating Systems |
Linux, Mac, Windows |
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Standard of De-Identification |
Incorporates S142 standards via CTP profiles |
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Support for multi-site submissions |
Yes |
Yes |
Yes |
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https://gforge.nci.nih.gov/frs/?group_id=312
http://www.kitware.com/products/midas.html