Christian Schmidt

About I3D:bio office, C. 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.

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, [...]

Introduction to Image Data Repositories and Public Archives

By |2023-11-29T16:47:42+01:00May 31st, 2023|

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 [...]

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