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: 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 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, [...]
Back to: Image Data Repositories The BioImage Archive - example of an archive-type image data repository Repositories provide long-term storage and access to published data, often in combination with minimun required metadata to make the data findable. There are many discipline-specific repositories for publishing scientific data as can be found using repository registries. However, [...]
Back to: Image Data Repositories Finding and Choosing a Data Repository What makes a good repository for imaging data? Public data sharing creates trust in scientific rigor, facilitates reproducibility and enables the potential reuse of data in other projects. Funding agencies may demand that original source data of a publication [...]
Back to: Image Data Repositories Introduction to Image Data Repositories and Public Archives Many bioimaging experiments are time-consuming and cost-intensive, and the acquired images are almost always subjected to image analysis to quantify image features of interest. Many imaging approaches thus produce large datasets, the value of which may extend [...]
https://zenodo.org/record/7018750#.Y4XEeHSZObg
