Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications

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 the 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.

Live cell microscopy: From image to insight

“…In addition to detailed reporting in the Methods section of any publication, this information should be stored in the raw image container (i.e., tiff) either directly or as additional (machine-readable) file. This will keep this crucial information connected to in the dataset, 168 which is helpful especially when uploading to a repository as described below.…”

MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text

“…MethodsJ2 and two companion software tools -Micro-Meta App 15 and OMERO. mde 23 -advance rigor and reproducibility in microscopy (Supplementary Fig.…”

“…Microscope manufacturers need to work with the global community through organizations such as Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy (QUAREP-LiMi) 24,25 to automate the collection of metadata, ensure they conform to community standards 4,6,23 and make them readily available. The implementation and evolution of MethodsJ2, Micro-Meta App 15 and OMERO.mde 23 , will promote transparency and reproducibility and help stakeholders to ensure that microscopy metadata are documented and reported.…”

“…MethodsJ2 automatically gathers metadata from the image using OME BioFormats (for example, pixel size, magnification) and captures microscopy metadata from a Microscope.JSON file generated using Micro-Meta App 5,15 . Micro-Meta App is a companion software tool that guides researchers step-by-step in the collection of community-standardized microscopy metadata for a specific microscope 4 .…”