| Literature DB >> 28187889 |
Tom Doel1, Dzhoshkun I Shakir2, Rosalind Pratt3, Michael Aertsen4, James Moggridge5, Erwin Bellon6, Anna L David7, Jan Deprest8, Tom Vercauteren2, Sébastien Ourselin2.
Abstract
OBJECTIVES: Clinical imaging data are essential for developing research software for computer-aided diagnosis, treatment planning and image-guided surgery, yet existing systems are poorly suited for data sharing between healthcare and academia: research systems rarely provide an integrated approach for data exchange with clinicians; hospital systems are focused towards clinical patient care with limited access for external researchers; and safe haven environments are not well suited to algorithm development. We have established GIFT-Cloud, a data and medical image sharing platform, to meet the needs of GIFT-Surg, an international research collaboration that is developing novel imaging methods for fetal surgery. GIFT-Cloud also has general applicability to other areas of imaging research.Entities:
Keywords: Anonymisation; Biomedical research; Cross-disciplinary research; Data sharing; Deidentification; Fetal surgery
Mesh:
Year: 2016 PMID: 28187889 PMCID: PMC5312116 DOI: 10.1016/j.cmpb.2016.11.004
Source DB: PubMed Journal: Comput Methods Programs Biomed ISSN: 0169-2607 Impact factor: 5.428
Fig. 1Simplified diagram illustrating collaboration using GIFT-Cloud. Data can be provided from hospitals as part of the routine workflow for patient care. Researchers can upload analysis of the data, which are then available to other collaborators. Confidential patient information never leaves the source hospital.
System requirements. This table describes the core hardware and software requirements for the components of the GIFT-Cloud system, and the current versions used in the GIFT-Cloud system installed at UCL.
| Minimum requirement | UCL system | |
|---|---|---|
| Operating system | Linux/Windows/macOS | CentOS Linux 7.2 |
| PostgreSQL | 9.1 | 9.2 |
| Oracle Java SDK | 1.7 | 1.7 |
| Apache Tomcat | 7.0 | 7.0 |
| XNAT | 1.6 | 1.6 |
| Operating system | Linux/Windows/macOS | Microsoft Windows Server 2008 R2 |
| Oracle Java JRE | 1.7 | 1.8 |
| Java Advanced Imaging | 1.1 | 1.1 |
| GIFT-Cloud Uploader | 1.1.10 | 1.1.10 |
Fig. 2Diagram showing the process for anonymisation and subject matching during upload of imaging data to GIFT-Cloud. Anonymisation is performed within the clinical institution; if uploaded via PACS this is performed by the Gateway server, while if the user uploads data directly from their computer then this anonymisation is performed on their local computer. Before uploading, the image metadata are examined to determine the type of anonymisation required. The Patient ID is translated into a pseudonymised patient identifier (PPID). This PPID is used to determine if the subject already exists on the server and to obtain the pseudonymous Research ID for that subject. If no subject exists, then a new subject is created with a new pseudonymous Research ID. Within the metadata, the Patient ID is replaced by the PPID and the patient name is replaced by the Research ID. Required data grouping fields such as the Series Instance UID are replaced with a SHA-1 hash of their value.
Fig. 3Illustration of automated pixel data anonymisation procedure applied before uploading images. The image shown is a cropped ultrasound scan of a training phantom. The image metadata are examined to determine if pixel data anonymisation is required. If so, a suitable template for the scanner model and image resolution is located that specifies which regions of the image contain personal identifiable data. These regions are blacked out before uploading. If no suitable template is found, the data are not uploaded.
Fig. 4The data access permissions model for GIFT-Cloud. In this example, the current data sharing agreements between institutions permit User 1 to access data from Institution A but not from Institution B. User 2 is permitted to access data from both institutions.
Fig. 5Data workflow showing how GIFT-Cloud is used in the development of an algorithm for placental segmentation for fetal surgery applications. The clinician uses the PACS to send a suitable dataset to GIFT-Cloud. The data are sent by DICOM Push to the GIFT-Cloud Gateway, which anonymises, encrypts and uploads the data to the GIFT-Cloud server. The researcher can then download the anonymised data, perform the segmentation and upload the resulting segmentation mask, which will be grouped in the same subject as the anonymised data. The clinician can now download and compare the anonymised data and segmentation for validation. Through such workflows GIFT-Cloud makes it possible to easily share new results during the active development stages of novel imaging methods.
Summary of GIFT-Cloud features including those provided by the XNAT system. GIFT-Cloud extends XNAT with additional tools and novel features. XNAT features labelled “via API” are not part of the standard XMAT 1.6 user interface but are available programmatically through the REST API and may be invoked by third-party tools such as those provided by GIFT-Cloud.
| Feature | XNAT 1.6 | GIFT-Cloud |
|---|---|---|
| Web user interface | ✓ | ✓ |
| REST API | ✓ | ✓ |
| Automatic subject grouping by PPID lookup | ✓ | |
| Interactive single-subject data upload | ✓ | ✓ |
| Automated multi-subject data upload | via API | ✓ |
| Remote DICOM Gateway for query/retrieve | ✓ | ✓ |
| Remote DICOM Gateway for anonymisation and store | ✓ | |
| PACS integration | via API | ✓ |
| PACS integration on-site anonymisation and encryption | ✓ | |
| Configurable client-side metadata anonymisation | ✓ | ✓ |
| Configurable client-side pixel data anonymisation | ✓ | |
| DICOM CT, MR, US support | ✓ | ✓ |
| NIFTI, Analyze support | via API | ✓ |
| Automatic MPEG to DICOM video conversion | ✓ |