Use Case 01: X-ray imaging
The advances in synchrotron imaging technology and experimental setups has open new avenues in biomedical research by offering levels of sensitivity and specificity in the investigation of biological tissue that overcome the performance of standard laboratory methods. Phase-contrast based synchrotron X-ray computed tomography (CT) have ushered in an era of non-invasive, three-dimensional visualization and navigation through tissue structures. This groundbreaking capability allows researchers to study tissue changes resulting from pathology and various treatments at the micro- to nano-scale. As a result, large amount of data are produced, up to several petabytes per year.
Effective management of such a substantial data influx requires tailored solutions for electronic data capture, coupled with robust data management and storage capabilities, as well as for the repository of processed (reduced) data and analysis codes to go with each publication to maximise data reuse and transparency.
By networking between user groups and scientists and IT experts from synchrotron facilities, the LMU and Göttingen teams aim at outlining a general FAIR data workflow for synchrotron imaging and CT experiments. Our objective is to gain knowledge and establish a consistent vocabulary, as well as a comprehensive list of parameters that can be applied across various beamlines and facilities. Together with other DAPHNE4NFDI members, we have finalized the metadata workflow and its description for a generic synchrotron imaging experiment. This work, included in the whitepaper, organizes all relevant parameters to be collected and stored, from the initial sample preparation phase to the experimental, data analysis, and publication stages.
We are actively working on the installation of SciCAT at our universities and the creation of repositories for sharing software within our community. Additionally, we are engaged in teaching and dissemination activities to promote the application of FAIR principles within our field.
