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Definition of project

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:

  1. to assess existing software and instantiations that are appropriate to their research or clinical needs.
  2. to locate relevant  publicly available data for research

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:

  1. Publicly hosted biomedical imaging archives which are populated with actual data which researchers, teachers, industry, etc may wish to utilize
  2. Image archive software solutions which one could download and use to host their own DICOM image data sets

Publicly Hosted Biomedical Imaging Archives

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 between August and October of 2010.  Some information was subsequently updated in July 2011.  See the wiki page history for a full log of the changes.

 

The Cancer Imaging Archive (TCIA)

NBIA

NIAMS

XNAT Central

Image Data Archive

Function BIRN Data Repository

NIRL Imaging Database

Give A Scan

Optical Society of America (OSA)

Pediatric MRI Data Repository

Insight Journal

National Database for Autism Research (NDAR)

Supporting Institution(s)

Cancer Imaging Program

Cancer Imaging Program, caBIG

NIAMS, caBIG

WUSTL, BIRN

Lab of NeuroImaging UCLA (LONI)

BIRN

BIRN

Lung Cancer Alliance, Kitware

Optical Society of America, Kitware

NIH, NDAR

Kitware

NIH

Content Type

In Vivo Cancer Imaging (see full Collection list)

In Vivo Cancer Imaging (see full collection list)

Osteoarthritis

Biomedical images and meta data

ADNI (Alzheimers),
CRYO (histology),
ICBM (Brain mapping),
AIBL (Autralian Aging)

Brain scans

ELUDE (Elderly Depression),
MIRIAD (Depression)

Patient-contributed Medical scans

Optical

Normal brain development 

Biomedical images and meta data

Autism - standard phenotypic data, imaging and genomic/pedigree data related to human subjects

Archive Software

NBIA

NBIA

NBIA

XNAT

Image Data Archive

custom

XNAT

MIDAS

MIDAS

custom

MIDAS

 

Login account required

Yes.  Accounts are free and available to anyone.

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.

 

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

 

Explicit data sharing policy

Yes, with options for uploading fully open or limited access data sets

Yes, with options for uploading fully open or limited access data sets

Yes, found here

No

 

 

 

 

 



 

Number of Registered Users (or NA)

764

 

 

 

 

 

 

 

 

 

 

 

Accepting new data

Yes (learn more)

Yes, with approval from NCI CBIIT/CIP

 

Yes, users can register accounts and upload data

 

 

 

Yes, through Lung Cancer Alliance

Yes, through the Optical Society of America


Yes, users can register accounts and upload data

 

Central curation/review

Yes, a trained staff visually inspects every image before making them visible

Yes, performed by CBIIT staff

 

No

 

 

 

Yes, performed by Lung Cancer Alliance

Yes, performed by the Optical Society of America


Yes, performed by Kitware staff and peer reviews

 

Availability/Uptime

~99%, hosted on a redundant production system at WUSTL

~99%, hosted on a redundant production system at NCI CBIIT

 

 

 

 

 

~99%, hosted on a production server at Kitware

~99.9%, hosted on a production server at OSA


~99%, hosted on a production server at Kitware

 

Project- or Collection- based groupings?

Yes

Yes

Yes

Yes

 

 

Yes

Yes

Yes


Yes

 

Size of Current Volume

7.3T

~2TB

~7.5TB

 

 

 

 

~2GB

~50GB


~60GB

 

Number of cases with imaging

~30,000

 

 

 

 

 

 

 

 

 

 

200

number of DICOM Tags query-able

~90

~90

~90

 

 

 

 

 

 



 

Data submission/download methods

Submission via DICOM or HTTPS protocols using CTP. Download via Java Webstart client

Submission via DICOM or HTTPS protocols using CTP. Download via Web (zip), FTP, Java Webstart client

Submission via DICOM or HTTPS protocols. Download via Web (zip), FTP, Java Webstart client

Submission via Web UI or DICOM protocol.  Download via Web (zip) or Java applet.

 

 

 

Submission via Web UI,
Download via Web (zip).

Submission via Web UI,
Download via Web (zip).


Submission via Web UI, DICOM push, MIDASDesktop, WebDAV.
Download via Web (zip), MIDASDesktop or WebDAV

 

Helpdesk Support

Yes, the TCIA Helpesk supports both end users and submitters

Yes, CBIIT Application Support

Yes, CBIIT Application Support

 

 

 

 

 

 

 

 

 

Affiliation with Journal

No

No

No

No

 

 

 

 

Yes



 

Intended Audience(s)

Cancer researchers, engineers and developers, professors

 

 

 

 

 

 

 

 

 

 

 

caBIG

NBIA

LONI

LONI homepage: http://www.loni.ucla.edu/

Image Data Archive - http://www.loni.ucla.edu/Research/Databases/

BIRN

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.

Insight Journal

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:

Lung Cancer Alliance: Give A Scan

http://www.giveascan.org/

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

Optical Society of America (OSA)

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.

WebMIRS

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.

NA-MIC Image Gallery

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.

Pediatric MRI Data Repository

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

NIH Image Bank

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.

European Organization for Research and Treatment of Cancer (EORTC)

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.

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.

 

NBIA

XNAT

MIDAS


 

 

Interface/GUI

Web

Web

Web/Desktop Application

 

 

 

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

Customizable, search by any tags registered in the system

 

 

 

Role Based Security

Yes

Yes

Yes

 

 

 

Public access option (no login req)

Yes

Yes

Yes

 

 

 

Active Development

Yes, NCI CBIIT

Yes, WUSTL Neuroinformatics Research Group

Yes, Kitware

 

 

 

License

Open source - NBIA License Agreement Details

Open source - XNAT License Agreement Details

non-restrictive (BSD) open-source license

 

 

 

Supports Federated Implementation

Yes, can discover other nodes on the caGrid

Not currently, but there are plans to add this functionality eventually

No

 

 

 

API available

Yes, caGrid

Yes, ?RESTFUL web services?

Yes, REST, OAI-PMH

 

 

 

Supported image formats

DICOM

 

DICOM and other ITK-based format

 

 

 

Supported metadata formats

XML, Zip

 

XML

 

 

 

Transfer protocols (import/export)

DICOM, HTTPS

 

HTTPS, DICOM

 

 

 

Controlled Vocabulary

Follows caBIG standards (caDSR/EVS)

 

NIH Mesh and Dublin Core

 

 

 

Deployment Support

Yes, CBIIT Application Support or via NBIA User Listserv

 

Yes, MIDAS mailing list

 

 

 

Support Operating Systems

Linux, Mac, Windows

Linux, Windows

Linux, Windows, Mac

 

 

 

Data submission options

Submission to NBIA is performed by a java tool called CTP developed out of RSNA.  CTP has options to import data from HDD or directly from a PACS or DICOM Workstation.

Direct upload is available through the web UI, direct DICOM transfer, or one could utilize the DICOM Browser java tool.

Direct upload via web UI, direct DICOM transfer via push, MIDASDesktop transfer (includes command line tools), WebDAV support.

 

 

 

Standard of De-Identification

Incorporates S142 standards via CTP profiles

No, but scripts based on standards could be written for DICOM Browser if desired

No, but pre-storage filters can be run automatically

 

 

 

Support for multi-site submissions

Yes

Yes

Yes

 

 

 

NBIA

https://gforge.nci.nih.gov/frs/?group_id=312

Xnat

http://www.xnat.org/

MIDAS

http://www.kitware.com/products/midas.html