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 [...]
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 includes the following steps (taken from: Schmidt & Ferrando-May, 2021) How to navigate the bioimage data life cycle? Any experiment starts [...]
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 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://gerbi-gmb.de/i3dbio/i3dbio-resources/metadata-guide/
https://gerbi-gmb.de/i3dbio/i3dbio-rdm/microscopyfileformats/
