Towards sharing and reusing of preclinical image data
Published: 2021-03-05
The preclinical imaging community faces many challenges when it comes to collecting, processing, and reusing the various types of imaging data produced in preclinical research. That is why a group from the Molecular Imaging Center (CIM) of the University of Torino, part of Euro-BioImaging’s Multi-Modal Molecular Imaging Italian Node, with support from the Horizon Europe EOSC-Life project, undertook the development of a user-friendly, customizable workflow to store, process and share preclinical image datasets through an XNAT-based platform available at http://cim-xnat.unito.it. These developments, along with analysis tools for automated image processing, will make it easier for preclinical imaging facilities to manage and process large, multi-modal imaging studies on an XNAT-based system. Depositing these datasets and making them available will promote data sharing among researchers and the reuse of imaging data, and thereby also reducing the need for new animal studies.
Read the preprint article here: https://arxiv.org/abs/2103.02044
Facilitating data sharing
As part of the EOSC-Life demonstrator project, a team of developers at University of Torino developed a suite of tools named XNAT-PIC (XNAT for Preclinical Imaging Centers) based on XNAT, a free and open-source imaging informatics platform that supports image data management and processing, to facilitate data sharing and reuse among preclinical imaging facilities.
Their achievements include coding a MRI2DICOM converter, so that Magnetic Resonance (MR) images in proprietary format can be converted to DICOM, the internationally-recognized standard for biomedical imaging. To facilitate the uploading of projects with multiple subjects, the team also designed an uploader for large, multimodal imaging studies. Finally, the team created dedicated image processing pipelines built on top of in-house scripts, to provide analysis tools for standardized, automated image processing and quantitative analysis.
Interested in trying it out?
All developments are freely available and can be accessed by clicking on the links below:
https://github.com/szullino/XNAT-PIC
https://github.com/szullino/XNAT-PIC-pipelines
For more information:
Sara Zullino, PhD
Molecular Imaging Center
Department of Molecular Biotechnology and Health Sciences
mailto: sara.zullino@unito.it
Twitter: https://twitter.com/szullina
LinkedIn: https://it.linkedin.com/in/sarazullino
About EOSC-Life
The European Open Science Cloud (EOSC) is a digital platform for the European science community, designed to give researchers from the European Union (EU) a global lead in research data management. Within this overarching project, EOSC-Life brings together the 13 Life Science Research Infrastructures (LS RIs) to create an open, digital and collaborative space for biological and medical research. This demonstrator project is an example of how EOSC-Life supports FAIR data principles, as applies to biomedical imaging. EOSC-Life receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824087.