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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

Publicly Hosted Biomedical Imaging Archives

 

NBIA

NIAMS

Central XNAT

Image Data Archive

Function BIRN Data Repository

NIRL Imaging Database]

Give A Scan

Optical Society of America (OSA)

Pediatric MRI Data Repository





Sponsor(s)

Cancer Imaging Program, caBIG

NIAMS, caBIG

BIRN

Lab of NeuroImaging UCLA (LONI)

BIRN

BIRN

Lung Cancer Alliance

Optical Society of America

NDAR





Content Type

In Vivo Cancer Imaging

Osteoarthritis

Osteoarthritis

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

Alzheimer's Medical Imaging

ELUDE (Elderly Depression),
MIRIAD (Depression)

Patient-contributed Medical scans

Autism Research

Autism





Archive Software

NBIA

NBIA

XNAT

Image Data Archive

custom

XNAT

MIDAS

MIDAS






Central curation/review

Yes

 

 

 

 

 

 

 






Explicit data sharing policy

Yes

 

 

 

 

 

 

 






Availability/Uptime

~99%

 

 

 

 

 

 

 






Submission Technology

CTP

 

 

 

 

 

 

 






Standard of De-Identification

Supplement 142 w/ Keep Description, Retain Device Info options enabled

 

 

 

 

 

 

 






Support for multi-site submissions

Yes

 

 

 

 

 

 

 






Project- or Collection- based groupings?

Yes

 

 

 

 

 

 

 






Size of Current Volume

~3TB

 

 

 

 

 

 

 






Federated implementation

Yes

 

 

 

 

 

 

 






number of DICOM Tags query-able

~90?

 

 

 

 

 

 

 






DICOM transfer protocol

For submission, but not download

 

 

 

 

 

 

 






methods to download DICOM data

Web, FTP, Java Webstart client

 

 

 

 

 

 

 






Affiliation with Journal

No

 

 

 

 

 

 

 






Support New Collection?

Yes

 

 

 

 

 

 

 






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.

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

National Alliance for Medical Image Computing (NA-MIC) Image Gallery: http://www.na-mic.org/publications/gallery

As of August 2010 this consisted of ~376 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

 

NBIA

XNAT

MIDAS


 

 

Interface/GUI

Web

Web

 

 

 

 

Query flexibility

Simple (9 parameters), Advanced (10 more parameters), Dynamic (boolean query of up to 90 DICOM tags)

 

 

 

 

 

Role Based Security

Yes

 

 

 

 

 

Public access option

Yes

 

 

 

 

 

Active Development

Yes

 

 

 

 

 

Supports Federated Implementation

Yes

 

 

 

 

 

API available

caGrid

 

 

 

 

 

Supported image formats

DICOM

 

 

 

 

 

Supported metadata formats

XML, Zip

 

 

 

 

 

Helpdesk support

Yes

 

 

 

 

 

Transfer protocols (import/export)

DICOM, HTTPS

 

 

 

 

 

Controlled Vocabulary

caBIG

 

 

 

 

 

Deployment Support

Yes

 

 

 

 

 

Support Operating Systems

Linux, Mac, Windows

 

 

 

 

 

NBIA

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

Xnat

http://www.xnat.org/
http://www.xnat.org/2010+XNAT+Workshop+Agenda

MIDAS

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