A deeper dive into metadata structures, and the OME data model How is metadata structured and stored in files? Metadata, i.e., the data providing essential accessory information about data (like image pixel values), can be structured in various ways. A specification for this structuring is defined by a data model, [...]
back to: BioImaging Metadata Why research-discipline-specific metadata standards are needed The FAIR (findable, accessible, interoperable, reusable) principles provide guidance in the form of general criteria for what renders data FAIR. However, no discrete technical adoption of these rather loosely defined criteria is provided. The reason is that no universal solution can meet [...]
Back to: Data Life Cycle Research data management for bioimaging confronts scientists and core facility staff with significant challenges. Orienting along the data life cycle concept for bioimaging data helps to create an overview and define necessary measures at research institutions to advance the data management capabilities. An asset is the implementation of a [...]
The NFDI4BIOIMAGE consortium, in which GerBI-GMB is a co-applicant, and the I3D:bio project, organize an online workshop about effective use of structured metadata annotations in OMERO to enhance the usability of imaging data for image analysis and publication. Two-Day-Workshop: April 29th & 30th. Online via Zoom. The workshop is targeted at researchers at all career levels using [...]
The image data management platform OMERO offers possibilities for structured metadata annotation. But with possibilities come decisions to make. Research projects are complex and, therefore, giving a unique one-size-fits-all recommendation for data structuring is difficult. Nevertheless, some basic principles for using structured annotations may help to shape your research data management to optimize usability. As [...]
The DFG-funded Information Infrastructure for BioImage Data (I3D:Bio) project arose from regular exchange within GerBI-GMB's working group Image Data Analysis and Management and meetings of the informal Research Data Management for Microscopy (RDM4mic) group. A key goal of I3D:bio is to facilitate research data management at universities and research institutions in Germany leveraging the image [...]
What are next-generation file formats (NGFF)? Structure of a classical file format As introduced in Bioimaging File Formats explained, microscopy image data can be written in various different file formats, mostly defined by the vendors of the microscopes used. Most of these files and also the "de facto" open community standard file "OME-TIFF" are [...]
Back to: Data Life Cycle The research data life cycle concept must be adapted to the specific needs of a research project. For research involving bioimaging techniques, a data life cycle for orientation is proposed below (adapted from Schmidt C and Ferrando-May E, 2021). How to navigate the [...]
Data management is made for bioimage analysts How often have you wondered about how to structure your folders, if you should write metadata within a single txt or json file or in one file for each image, how to name your images consistently so that your code will be able to find them? Well all [...]
Back to: Image Data Repositories The Image Data Resource - example of an added-value database At present, many repositories recommend but do not enforce to use of specific metadata items or formats when submitting bioimaging data. Mostly, also the file format can be chosen at the submitter‘s discretion. However, to make data Findable, Accessible, Interoperable, [...]
