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  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 tables is an analysis of what was found upon reviewing each archive between August and October of 2010.  Information in the tables are being updated semi-regularly, but the Additional Details section below is not.  See the wiki page history for a full log of the changes.  Please notify kirbyju@mail.nih.gov or freymanj@mail.nih.gov to report errors, additions, etc.  

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The Cancer Imaging Archive (TCIA)

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NBIA

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NIAMS

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XNAT Central

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Image Data Archive

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Function BIRN Data Repository

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NIRL Imaging Database

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Give A Scan

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Optical Society of America (OSA)

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Insight Journal

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National Database for Autism Research (NDAR)

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Supporting Institution(s)

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Cancer Imaging Program

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Cancer Imaging Program, caBIG

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NIAMS, caBIG

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WUSTL, BIRN

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Lab of NeuroImaging UCLA (LONI)

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BIRN

...

BIRN

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Lung Cancer Alliance, Kitware

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Optical Society of America, Kitware

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Kitware

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NIH, NIMH, NINDS, NICHD, NIEHS

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Content Type

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In Vivo Cancer Imaging and related phantom data (see full Collection list)

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In Vivo Cancer Imaging (see full collection list)

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Osteoarthritis

...

Biomedical images and meta data

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

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Brain scans

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ELUDE (Elderly Depression),
MIRIAD (Depression)

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Patient-contributed Medical scans

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Optical

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Biomedical images and meta data

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

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Normal brain development

 

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Archive Software

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NBIA, AIM Data Service (XML image metadata), and a Clinical Data relational database

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NBIA

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NBIA

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XNAT

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Image Data Archive

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custom

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XNAT

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MIDAS

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MIDAS

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MIDAS

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Login account required

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Yes.  Accounts are free and available to anyone. Click here to register.

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For advanced site features or limited access data sets, but is not required for accessing public data. Click here to register.

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Yes. Click here to register.

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For accessing limited access data sets, but not for public data

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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

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No

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For accessing limited access data sets, but not for public data

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For accessing limited access data sets, but not for public data

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Yes

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Explicit data sharing policy

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

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

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Yes, found here

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No, data is made public or restricted as specified by the user who uploads it.

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...

 

...

 

...

All data is made publicly accessible.

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...

 

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Yes, found here

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Number of Registered Users (or NA)

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2,333

...

 

...

 

...

 

...

 

...

 

...

 

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N/A

...

 

...

 

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60 for data access
100-200 for data submission

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Accepting new data

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Yes, proposals are accepted via email and reviewed monthly by the TCIA Advisory Committee. Acceptance criteria is summarized here: Requesting Permission to Upload your Data.

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Yes, with approval from NCI CBIIT

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...

Yes, users can register accounts and upload data

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...

 

...

 

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Yes, through Lung Cancer Alliance. Learn more here.

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Yes, through the Optical Society of America

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Yes, users can register accounts and upload data

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Yes, learn more here

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Central curation/review

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Yes, a multiple tiered de-identification and QC process is utilized involving both human review and systematic analysis.  The process is summarized in detail on the TCIA De-Identification Knowledge Base and What to Expect as an Image Provider.

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Yes, performed by CBIIT staff

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...

No

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...

 

...

 

...

Yes, performed by Lung Cancer Alliance

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Yes, performed by the Optical Society of America

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Yes, performed by Kitware staff and peer reviews

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Yes, pre-validation is performed to ensure all data conforms/harmonizes to the autism data dictionary. QA is also performed by NDAR staff to check for identifiable information.

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Availability/Uptime

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

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

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

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...

 

...

 

...

 

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~99%, hosted on a production server at Kitware

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~99.9%, hosted on a production server at OSA

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~99%, hosted on a production server at Kitware

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~99%, imaging data hosted on Amazon and metadata hosted by NIH.

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Project- or Collection- based groupings?

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Yes

...

Yes

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Yes

...

Yes

...

 

...

 

...

Yes

...

Yes

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Yes

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Yes

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Yes

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Size of Current Volume

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TCIA: 1.36 TB
NLST-LSS: 6.47 TB
NLST-ACRIN: 4.8 TB

Total: 12.63 TB

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~2TB

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~7.5TB

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...

 

...

 

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33GB

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~50GB

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~60GB

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~2TB

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Number of patients/subjects with imaging

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TCIA: 3,166
NLST-LSS: 17,043
NLST-ACRIN: 9,204

Total: 29,413

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5,096

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4,796

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3,494

...

 

...

 

...

 

...

37

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...

 

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2500 NDAR

 

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Number of DICOM Tags query-able

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~90 via NBIA

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~90

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~90

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...

 

...

 

...

 

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22 (imaging parameters in query interface)

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9, with full listing from data dictionary. (4 NDAR, 5 Pediatric MRI)

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Some unstructured clinical data such as patient age, cancer stage, recurrence, and treatment information.

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Data submission/download methods

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Submission via DICOM or HTTPS protocols using CTP. Download via Java Webstart client. A REST API is in development with an expected public release in the summer of 2013.

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

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

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

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

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

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

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Sites do their own de-identification any way they prefer, so long as it meets their IRB's approval.  They can optionally use MIPAV for this part of the process.  Submissions must conform to NDAR Data Dictionary. A custom Java Webstart application allows SFTP transfers. 

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Helpdesk Support

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Yes, the TCIA Helpdesk supports both end users and submitters. They provide phone and email support during regular business hours Mon-Fri.

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Yes, CBIIT Application Support

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Yes, CBIIT Application Support

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No official helpdesk info found on the site.  Some support may be available from giveascan@lungcanceralliance.org.

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Yes, available at ndarhelp@mail.nih.gov.

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Affiliation with Journal

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No

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No

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No

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No

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...

 

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No

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Yes

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No

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Please contact Justin Kirby (kirbyju@mail.nih.gov) or John Freymann (freymanj@mail.nih.gov) with any questions, error reports, updates, additions, etc. 

Acknowledgements

We would like to thank the following people for volunteering their time and effort in helping us populate this survey.

  • Dan Marcus (WUSTL)
  • Brian Hughes (Terpsys)
  • Dan Hall (NIH)
  • Patrick Reynolds (Kitware)
  • Julien Jomier (Kitware)
  • Ivo Dinov (UCLA)
  • Matthew McAuliffe (NIH)
  • David Keator (UCI)
  • Christian Haselgrove (NITRC)

Publicly Hosted Biomedical Imaging Archives

The following table attempts to summarize publicly accessible biomedical image archives.  This survey originally initiated in August of 2010.  Information in the tables are being updated periodically.  

NOTE: Due to the large size of this table you may need to use the horizontal scroll bar at the bottom of the table to view some of the archives listed furthest to the right.

 

The Cancer Imaging Archive (TCIA)

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NBIA

NIAMS

XNAT Central

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Image Data Archive

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Function BIRN Data Repository

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Give A Scan

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Optical Society of America (OSA)

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Insight Journal (MIDAS)

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National Database for Autism Research (NDAR)

Pediatric MRI Data RepositoryFITBIRNITRC-IR
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Supporting Institution(s)

NCI Cancer Imaging Program

NCI Center for Bioinformatics and Information Technology

NIAMS, NCI Center for Bioinformatics and Information Technology

WUSTL, BIRN

Lab of NeuroImaging UCLA (LONI)

FBIRN Institutions

Lung Cancer Alliance, Kitware

Optical Society of America, Kitware

Kitware, Insight Software Consortium

NIH, NIMH, NINDS, NICHD, NIEHS

NIH, NIMH, NICHD, NIDA, NINDSNINDS, DoDNIH Blueprint, NIBIB, NINDS, NIMH, NIDA

Content Type

In Vivo Cancer Imaging, phantom imaging and related metada (see full Collection list)

Demo instance for showing the latest features of NBIA.  All data are re-used from The Cancer Imaging Archive.

Osteoarthritis

Biomedical images, meta data, other phenotypic data (behavioral, clinical, etc)

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

FMRI/MRI images, behavioral data, and clinical data from schizophrenics and healthy volunteers.  Willing to accept data on other neurological disorders.

 

Patient-contributed Lung Cancer Medical scans

Optical, digital holography, 2D/3D modalities, etc

Biomedical images, meta data, and journal articles

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

Normal brain development

 

TBI related data: imaging, phenotypic and some genomics; human but expanding to preclinical modelsNeuroimages

Archive Software

NBIA, AIM Data Service (XML image metadata), and a Clinical Data relational database

NBIA

NBIA

XNAT

Image Data Archive

Human Imaging Database (HID)

MIDAS

MIDAS

MIDAS

customSame as NDAR (custom)Biomedical Research Informatics Computing System (BRICS) NIH developed – customXNAT

Login account required

No.  Public data is accessible without logging in.  Some special restricted-access data sets do require free registration. Register on the TCIA website.

For advanced site features or limited access data sets, but is not required for accessing public data. Click here to register.

Yes. Register on the NIAMS website.

For accessing limited access data sets, but not for public data

Yes, via web https://ida.loni.ucla.edu/login.jsp
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No (email requested)

No

For accessing limited access data sets, but not for public data

Only for submitting data.

Yes

YesYesFor accessing limited access data sets, but not for public data

Explicit data sharing policy

Yes

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, 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, data is made public or restricted as specified by the user who uploads it.

Yes. IDA User Manual.

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All data is made publicly accessible.

All data is made publicly accessible.

Yes, found here

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All data is made publicly accessible (varying licenses)

Yes, found here

Similar to NDAR but there is no explicit policyYes, https://fitbir.nih.gov/jsp/about/policy.jspNo

Number of Registered Users (or NA)

6,117

2,712

46

~1,000

>1,000

N/A

N/A

 

2,657

60 for data access
100-200 for data submission

~30

15 – just starting

1976 users as of April, 2015

Accepting new data

Yes, proposals are accepted via email and reviewed monthly by the TCIA Advisory Committee. Acceptance criteria is summarized here: Requesting Permission to Upload your Data

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No

More data is being added as part of the official initiative, but external proposals are not being accepted.

Yes, users can register accounts and upload data

Yes, see section 9 in the Appendix of the LONI Policies & Procedures

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Yes, https://www.birncommunity.org/about/contact/

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Yes, through Lung Cancer Alliance. Learn more here

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Yes, new data may be added as part of future Optical Society of America publications are released.

Yes, users can register accounts and upload data.

Yes, learn more here

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NoYes, FITBIR has established a two-tiered submission strategy to ensure high quality and to provide maximum benefit to investigators.  See the Data Submission Procedures for more information.Yes.  Community-generated data sets may be suggested for inclusion.  Contact moderator@nitrc.org.

Central curation/review

Yes, a multiple tiered de-identification and QC process is utilized involving both human review and systematic analysis. The process is summarized in detail on the TCIA De-Identification Knowledge Base and What to Expect as an Image Provider

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No

Yes, performed by NIAMS staff.

No

Collaborators strip all personal info from data prior to submission to LONI. Then LONI auto filters again, to ensure that there are no PHI in the files (especially if the data is binary) and stores the data in quarantine, until it’s approved for posting to the web interface.

PHI must be removed by the submitting institution prior to giving the data to the FBIRN.

FBIRN also performs a review to make sure there aren't any de-identification problems.

Yes, performed by Lung Cancer Alliance

Yes, performed by the Optical Society of America

Yes, some QC performed by Kitware staff and peer reviews.  Most data is de-identified by the submitter prior to upload.

Sites do their own de-identification any way they prefer, so long as it meets their IRB's approval. 

Pre-validation is performed to ensure all data conforms/harmonizes to the autism data dictionary. QA is also performed by NDAR staff to check for identifiable information.

Archived project, no longer receiving new data.Yes, pre-validation is performed to ensure all data conforms to the NINDS CDEs. QA is also performed by staff to check for personal identifiable information.Yes, performed by NITRC.

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 redundant production system at NCI CBIIT

~99%

Continuous (no exact % specified)

Continuous (no exact % specified)

~99.9%, hosted on a production server at Kitware

~99.9%, hosted on a production server at OSA

~99%, hosted on a production server at Kitware

~99%, imaging data hosted on Amazon and metadata hosted by NIH.

~99%, hosted by NIH.~99%, hosted by NIH.~99.9%, hosted on production servers at UCSD.

Project- or Collection- based groupings?

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

Yes

NoYesYes

Size of Current Volume

TCIA: 2.26 TB

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NLST-LSS: 6.5 TB
NLST-ACRIN: 4.8 TB
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Total: 13.56 TB

~21GB

~7.5TB

1 TB

0.7 PB

~2TB

33GB

~50GB

~60GB

~2TB

~2TB0.5TB1.5 TB

Number of patients/subjects with imaging

TCIA: 5,997

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NLST-LSS: 17,043
NLST-ACRIN: 9,211
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Total: 32,251

32

4,796

3,494

> 120,000

~300

37

N/A

> 200, plus some non-patient data

2500 NDAR

 

550 (migrated into NDAR)2006854 subjects

Number of DICOM Tags query-able

2 via the Simple Search, ~90 via the Advanced Search, and all DICOM metadata can be queried using the Text Search option.

2 via the Simple Search, ~90 via the Advanced Search, and all DICOM metadata can be queried using the Text Search option.

~90

~50

50

0

22 (imaging parameters in query interface)

N/A

22 (imaging parameters in query interface)

9, with full listing from data dictionary. (4 NDAR, 5 Pediatric MRI)

9, with full listing from data dictionary. (4 NDAR, 5 Pediatric MRI)10N/A
Metadata AvailabilityWide variety of clinical, genetic, and image segmentation/annotation available is available for various data sets.  Full summary can be viewed here
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in the "Supporting Data Available" column.
NoneNone

Various clinical and other metadata

Biospecimen, clinical, pathological, neuropsychiatric, and demographic.Yes, extensive behavioral data and clinical data. 

Some unstructured clinical data such as patient age, cancer stage, recurrence, and treatment information.

Associated articles, figures, publication-specific metadata, etcUnstructured clinical data as well as publication-specific metadata

NDAR contains all human subjects data related to autism research funded by the NIH and others.  Outside of the NDAR data dictionary, Metadata supporting project definition and research results are provided (see data from papers). 

 

 

Yes, all metadata is collected using NINDS CDEs

Gender, age, handedness, diagnosis, and MR acquisition parameters. Various cognitive assessments and other rich metadata available for some data.

Data submission/download methods

Submission via DICOM or HTTPS protocols using CTP

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. Download via Java Webstart client. A REST API is also available with documentation.

Submission via DICOM or HTTPS protocols using CTP

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. Download via Web (zip), FTP, Java Webstart client

Submission via DICOM or HTTPS protocols using CTP

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. Download via Web (zip), FTP, Java Webstart client

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

Secure web upload

Downloads via Web UI, Submissions via https://www.birncommunity.org/about/contact/

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

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

Submission via Web UI, DICOM push, MIDASDesktop.


Download via Web (zip), MIDASDesktop

A custom Java Webstart application allows SFTP/Amazon S3 transfers.  MIPAV is offered as an optional method for de-identification.  Submission is harmonized to the autism data standard using custom data validation software. 

Download methods include multithreaded download from the Amazon Cloud or push to cloud computational pipeline.

Not applicable.They can use MIPAV for submitting images. Submissions must conform to FITBIR Data Dictionary (NINDS CDEs). A custom Java Webstart application allows SFTP transfers.Upload by arrangement.  Download via Web (zip), Java applet, or REST API.

Helpdesk Support

Yes, the TCIA Helpdesk 

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supports both end users and submitters. They provide phone and email support during regular business hours Mon-Fri.

Yes, CBIIT Application Support

Yes, CBIIT Application Support

Via XNAT discussion group

dba@loni.ucla.edu

Yes, via https://www.birncommunity.org/about/contact/

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Technical issues can be sent to midas@public.kitware.com or click here for  Administrative support and other questions

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Contact infobase@osa.org.

Contact midas@public.kitware.com

Yes, available at ndarhelp@mail.nih.gov.

Yes, pedsmri@mail.nih.gov.Yes, FITBIR-help@mail.nih.govContact moderator@nitrc.org.

Affiliation with Journal

Not directly, but Digital Object Identifiers can be provided for integration with publications.  TCIA is also a recommended repository for Nature's Scientific Data journal.

No

No

No

Yes, NeuroImage

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No

No

Yes, Optics Info Base

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Yes, Insight Journal

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No

NoNoNo

Intended Audience(s)

Cancer researchers, engineers and developers, professors

Cancer researchers and anyone Anyone interested in testing the functionality of the NBIA software.

Osteoarthritis researchers

 

 

 

 All imaging research

Neuroimaging and genetics research

Neuroimaging research

Lung cancer researchers

 

 

researchers

Optical Society of America subscribers

All imaging research

Autism researchers (clinical/phenotype/genomic), both those receiving autism related NIH grants and other investigators sponsored by an NIH recognized institution with a current federal-wide assurance.

Neuroscientists interested in normative brain study of child development. TBI researchers Neuroimaging research


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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.

...

Software Name and Web Site

...

NBIA

...

XNAT

...

the software.

Software Name and Web Site

NBIA GForge project

XNAT

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MIDAS

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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 provideExtensible set of DICOM tags as well as linked quantitative biomarkers, linked clinical data, and other non-imaging data.

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

Non-restrictive (BSD) open-source license - XNAT License Agreement Details

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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, caGridREST

Yes, REST

Yes, REST, OAI-PMH

Supported image formats

DICOM

Automated import of DICOM and ECAT. Custom importers can be implemented for other formats.  Any file type can be uploaded through the API and web interface.

DICOM and other ITK-based format

Supported metadata formats

XML, Zip

XML, CSV. Custom data import logic can be implemented via pluggable Groovy and Python scripts.

XML

Transfer protocols (import/export)

DICOM, HTTPS

DICOM, HTTPS

DICOM, HTTPS

Controlled Vocabulary

Follows caBIG standards (caDSR/EVS)

XNAT Schema

NIH Mesh and Dublin Core

Deployment Support

Yes, CBIIT Application Support or via NBIA User Listserv

XNAT Google Discussion group, monthly developer tcons, biannual user conference. Commercial technical support provided by Radiologics.

Yes, MIDAS mailing list

Support Operating Systems

Linux, Windows, Mac

Linux, Windows, Mac

Linux, Windows, Mac

Data submission optionsSubmission to NBIA is performed by a java tool called CTP options

Submission to NBIA is performed by a java tool called CTP

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developed by John Perry at the RSNA.  CTP has options to import data from a hard drive or directly from a PACS or DICOM Workstation.

Direct upload is available through the web UI, direct DICOM transfer, scripts using REST API., optimized CTP workflow

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

Standard of De-Identification

Incorporates DICOM de-identification standards from The Attribute Confidentiality Profile (DICOM PS 3.15: Appendix E) via CTP.

Built-in de-identification language based on DICOM Browser

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can be configured to comply with DICOM PS 3.15: Appendix E and other standards.

No, but pre-storage filters can be run automatically

Support for multi-site submissions

Yes

Yes

Yes

 

 

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