@article {67305, title = {Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications}, journal = {bioRxiv}, year = {2021}, month = {2021 May 31}, abstract = {

For the information content of microscopy images to be appropriately interpreted, reproduced, and meet FAIR (Findable Accessible Interoperable and Reusable) principles, they should be accompanied by detailed descriptions of microscope hardware, image acquisition settings, image pixel and dimensional structure, and instrument performance. Nonetheless, the thorough documentation of imaging experiments is significantly impaired by the lack of community-sanctioned easy-to-use software tools to facilitate the extraction and collection of relevant microscopy metadata. Here we present\ Micro-Meta App, an intuitive open-source software designed to tackle these issues that was developed in the context of nascent global bioimaging community organizations, including\ BioImaging\ North\ America (BINA) and\ QUAlity Assessment and\ REProducibility in\ Light\ Microscopy (QUAREP-LiMi), whose goal is to improve reproducibility, data quality and sharing value for imaging experiments. The App provides a user-friendly interface for building comprehensive descriptions of the conditions utilized to produce individual microscopy datasets as specified by the recently proposed 4DN-BINA-OME tiered-system of Microscopy Metadata model. To achieve this goal the App provides a visual guide for a microscope-user to: 1) interactively build diagrammatic representations of hardware configurations of given microscopes that can be easily reused and shared with colleagues needing to document similar instruments. 2) Automatically extracts relevant metadata from image files and facilitates the collection of missing image acquisition settings and calibration metrics associated with a given experiment. 3) Output all collected Microscopy Metadata to interoperable files that can be used for documenting imaging experiments and shared with the community. In addition to significantly lowering the burden of quality assurance, the visual nature of Micro-Meta App makes it particularly suited for training users that have limited knowledge of the intricacies of light microscopy experiments. To ensure wide-adoption by microscope-users with different needs Micro-Meta App closely interoperates with\ MethodsJ2\ and\ OMERO.mde, two complementary tools described in parallel manuscripts.

}, author = {Alex Rigano and Shannon Ehmsen and Serkan Utku Ozturk and Joel Ryan and Alexander Balashov and Mathias Hammer and Koray Kirli and Karl Bellve and Ulrike Boehm and Claire M. Brown and James J. Chambers and Robert A. Coleman and Andrea Cosolo and Orestis Faklaris and Kevin Fogarty and Thomas Guilbert and Anna B. Hamacher and Michelle S. Itano and Daniel P. Keeley and Susanne Kunis and Judith Lacoste and Alex Laude and Willa Ma and Marco Marcello and Paula Montero-Llopis and Glyn Nelson and Roland Nitschke and Jaime A. Pimentel and Stefanie Weidtkamp-Peters and Peter J. Park and Burak Alver and David Grunwald and Caterina Strambio-De-Castillia} }