Christian Schmidt

About Christian Schmidt

Contributions by the I3D:bio office are drafted by Christian. Texts are reviewed by members of the I3D:bio team or external collaborators. Feedback welcome.

Workshop Announcement: FAIR data handling in microscopy – Structured metadata annotation in OMERO

By |2024-03-18T15:39:53+01:00March 18th, 2024|

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 [...]

I3D:bio’s OMERO training material available

By |2023-11-16T15:06:44+01:00November 16th, 2023|

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 [...]

Next-generation file formats for bioimaging

By |2023-10-05T10:53:03+02:00October 2nd, 2023|

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 [...]

Featured Repository: The Image Data Resource

By |2023-06-12T14:42:13+02:00June 2nd, 2023|

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, [...]

Featured Repository: The BioImage Archive

By |2023-06-12T14:42:13+02:00June 2nd, 2023|

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, [...]

Finding and Choosing a Repository

By |2023-06-02T15:02:46+02:00June 1st, 2023|

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 [...]

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