Preclinical imaging centers deal with many challenges mostly related to the variety of imaging instrumentation yielding huge volumes of raw data. The current procedures to collect, share and reuse preclinical image data are insufficient, thus revealing an urgent need of standardization in terms of data storage and image processing. XNAT for Preclinical Imaging Center (XNAT-PIC) has been developed to overcome this limitation by extending XNAT’s basic functionalities to meet the needs of preclinical imaging facilities. XNAT (www.xnat.org) is a popular open-source imaging informatics platform to store, process and share image-related studies.
XNAT-PIC is a suite of tools developed for XNAT-based platforms to support preclinical imaging. It consists of
• MRI2DICOM, a Magnetic Resonance Imaging converter from ParaVision® (Bruker, Inc. Billerica, MA) file format to DICOM standard
• XNAT-PIC Uploader to import multi-modal imaging studies with multiple subjects to XNAT
• XNAT-PIC Pipelines, a set of processing pipelines built on top of in-house scripts than can be easily tailored to your needs.
Generic XNAT users can sign up to our CIM-XNAT instance at http://cim-xnat.unito.it, upload the MR image datasets to be analyzed and add the pipelines to their own projects. XNAT admins can download the XNAT-PIC pipelines from the GitHub repository, install and register them in their own XNAT instance. The scripts developed for the XNAT-PIC project are available at the following GitHub repositories where users can also find a complete installation guide:
Our experience in EOSC-Life was great! The interaction with EOSC-Life technical experts was always inspiring and productive. Based on our experience, the possibility to access EOSC-Life expertise, resources and funding shortened the time to carry out our project. We had the opportunity to network with several scientists and established close cooperation with their Research Infrastructures. Moreover, attending training events and hackathons was a fantastic occasion to build knowledge and share expertise. Thanks to EOSC-Life, XNAT-PIC has already attracted interest from several European preclinical imaging centers!
– Sara Zullino
UNITO (Sara Zullino, Alessandro Paglialonga, Walter Dastrù, Silvio Aime)
IBB-CNR (Dario Livio Longo)
(Preprint) Sara Zullino, Alessandro Paglialonga, Walter Dastrù, Dario Livio Longo, and Silvio Aime. XNAT-PIC: Extending XNAT to Preclinical Imaging Centers. DOI: arxiv.org/abs/2103.02044