Stanford Medicine Research Data Repository (STARR) is integrated with hospital systems that store radiology, cardiology and retinal fundus imaging DICOM data.
Imaging
About imaging data
Radiology DICOMs: Radiology data from both hospitals are stored in a common Sectra PACS. The Sectra PACS replaced the shared GE PACS. All data from GE were migrated to Sectra. Data in Sectra PACS is replicated in the Vendor Neutral Archive (VNA). For the last several years, Research IT has built up the radiology data lake lake by query/retrive (Q/R) from GE and Sectra PACS. STARR data lake now has historical radiology data, since 2011. Earlier in 2020, we achieved a complete integration with VNA and now new radiology data collected daily is pushed nightly to STARR from the VNA.
Cardiology DICOMs and Syngo Database: The two hospital systems have two distinct Cardiology PACS systems, children's hospital Syngo application and adult hospital Syngo application. The DICOM data stored in Syngo are not available in the vnedor neutral archive (VNA). STARR has query/retrieve (Q/R) access to these two cardiology PACS. At this time, the cardiology imaging data is procured when there is an active consultation request from the researcher.
Fundus DICOMs: SHC uses Zeiss application in ENT for retinal fundus imaging. Some of this data is in VNA and is accessible via Query/Retrieve. A subset of the retinal imaging devices don't have integration with VNA at the time of writing. At this time, the retinal imaging data is procured when there is an active consultation request from the researcher.
At Stanford, the radiology PACS is Sectra (previously GE), the Cardiology PACS is Syngo, the ENT mini-PACS is Zeiss and the VNA is Fuji. Bulk of the VNA data is Radiology. While X-rays form bulk of the studies (accession IDs), the bulk of the images are CT or MRI. Adhoc pull implies query/retrieve and is launched when researchers request data. STARR also receives nightly data from the VNA, the new daily data is batched up and sent to STARR every night.
Access to imaging data
Researchers can request following services for imaging data via a data service consultation request:
- DICOMs from following systems
- Multi-modal radiology imaging data (X-rays, CTs, MRIs, Ultra sounds, ...) from both hospitals
- Echocardiograms from both hospitals
- Retinal images from adult hospital
- Identified or de-identified DICOMs (using accession_ids or MRNs if available)
- A human subject data (either identified or de-identified) is accessible with an approved IRB.
- A limited data set is accessible with an approved eprotocol.
- Cohort identification using STARR Tools or OMOP or Montage (SHC Radiology only).
- Linked EHR data from OMOP or Stanford data model (STARR Tools data model).
- If a radiology study needs access to Quality and Research (QR) PACS, it is possible to request delivery to QR PACS. Our general practice is to deliver the data to Box (small number of studies) or Nero (large number of studies).
- Content from LPCH Cardiology PACS Syngo database. The database contains labels and annotations such as left and right ventricle heart rate, ejection fraction, diastolic area etc.
DICOM de-identification
Research IT has developed highly sophisticated petascale DICOM de-identification pipeline that leverages and extend MIRC CTP.
Learn more about our methods.