MRS on VIP

The Virtual Imaging Platform (VIP) is a web portal for medical imaging applications. It allows its more than 1500 users to access scientific applications as a service, as well as distributed computing resources in a transparent manner. It exploits the resources available in the biomed virtual organisation of the EGI e-infrastructure to offer an open service to researchers worldwide.

Magnetic resonance spectroscopy (MRS) is a medical imaging technique that exploits the magnetic properties of biological tissues to determine their chemical composition. In particular, we can use the magnetic resonance signal to estimate in vivo the concentration of certain metabolites (e.g.: neurotransmitters, amino acids) at a certain location in the body (e.g.: a region of the brain). This requires specific acquisition protocols and reconstruction and quantification pipelines that need to be studied to increase the robustness, reproducibility and reliability of measurements.

This use case covers the whole MRS data lifecycle, from acquisition to storage, management, analysis and reuse. Data is acquired on the PILoT facility and stored in a Girder warehouse with associated metadata. Data is then processed with tools available on VIP and results are pushed back to the Girder warehouse.

The Girder platform stores data enriched with metadata, allowing for data management, access and discovery. Girder is also integrated with VIP, which provides a catalogue of available tools (which can be easily enriched with new ones) and a set of reproducibility services, such as a reproducibility dashboard or the possibility to “publish” results on Zenodo.

This use case encompasses the entire MRS data lifecycle, from acquisition to storage, management, analysis, and reuse. Data is acquired at the PILoT37 facility and stored in a Girder warehouse, along with associated metadata. Data is then processed with tools available on VIP, and results are pushed back to the Girder warehouse.
The Girder platform stores data enriched with metadata, enabling efficient data management, access, and discovery. Girder is integrated with VIP, which provides a catalogue of available tools and a set of reproducibility services, including a reproducibility dashboard and the ability to “publish” results on Zenodo.
The baseline use case is the following:

• The researcher has a Girder and a VIP account. They know precisely what data they want to analyse, as well as what pipelines they need to analyse the data.
• The researcher selects the data on Girder and the corresponding pipeline on VIP, and then launches the execution.
• The researcher retrieves the results.

• Integrate EOSC Data Commons tools for data discovery and FAIRness
• Automate data (format) discovery and tool selection
• Make the tools available in production for a larger community

EOSC Matchmaker
Contribute to the Catalogue of Tools by publishing applications available in VIP. The use case will also make MRS data discoverable using the services offered by the project. By integrating the EOSC Matchmaker with VIP, researchers should be able to pair data with ready-to-use processing tools.

EOSC Data Player
VIP will be integrated with the EOSC Data Player allowing it to execute Packages for Processing Datasets, making it easier for users in EOSC to analyse MRS datasets.

FAIR Assessment Toolkit
Plan to integrate VIP with the FAIR Assessment Toolkit to evaluate and improve the FAIRness of MRS datasets.