A collaborative project to make FLIM bioimage datasets more FAIR

Our seventh featured Data Steward is Cornelia Wetzker. She is a biologist trained in molecular biology, immunology and zoology, and works at the Center for Molecular Bioengineering (B CUBE) at TU Dresden. Conni shares how she led a project to make bioimage data from fluorescence lifetime imaging microscopy (FLIM) more FAIR. In close exchange with NFDI4BIOIMAGE colleagues, Conni created a workflow and plugin for the open-source 3D viewer napari that allow the import and analysis of FLIM data. Worksflows and data are shared openly. Learn more about the project and be inspired to contribute to similar work:

Conni is a cell biologist by training experienced in life science research and the microscopy facility work. As a data steward in bioimaging she benefits from her professional career stages providing her the combination of the scientific, technical but also data science perspectives of projects. Today, she combines the aspects of research, support as well as the education of especially young scientists to better integrate the FAIR principles into life science research. Prior to the project, FLIM bioimage data has been typically saved in formats of the microscope vendors rather than open and interoperable community formats and largely is today. This limits the options to visualize and analyze FLIM datasets for best scientific output and reuse of the data. Today, more and more scientists, facility staff but also company representatives contribute to a change of data formats in FLIM microscopy. About three years ago, an interdisciplinary team including Marcelo Zoccoler, Gunar Fabig and Conni set out to develop a workflow to convert FLIM data to an open format importable into community-developed platforms and tools for bioimage data handling and analysis. The team combined expertise in C. elegans biology, advanced bioimaging and bioimage data handling, analysis as well as scientific software development. This led to a fruitful project covering all stages from experimental work to data processing and creation of a napari plugin to convert FLIM data, phasor analysis using napari and data deposition in public repositories and platforms. Along the project, the raw to processed datasets including workflows and source code were continuously documented and made openly available for future reuse and further development of conversion and analysis workflows including OMERO, GitHub, zenodo, bioimage repositories such as BioImage Archive and SSBD. Along the project, Conni and co-workers closely interacted with colleagues within NFDI4BIOIMAGE regarding (next-generation) file formats and metadata annotations in OMERO. Overall, the interdisciplinary and collaborative co-work was the basis of this successful project. Read and learn more about the final publication of the project in the Journal of Microscopy. Reach out in case of questions and feedback and contribute to make bioimaging FAIRer.