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://gerbi-gmb.de/i3dbio/i3dbio-resources/metadata-guide/
https://gerbi-gmb.de/i3dbio/i3dbio-rdm/microscopyfileformats/
https://zenodo.org/record/7018750#.Y4XEeHSZObg
Back to: Microscopy File Formats Translating Bioimaging File Formats with "Bio-Formats" The Open Microscopy Environment Consortium has created the so-called Bio-Formats library (Linkert et al., 2010, J Cell Biol) to enable the translation from a large number of proprietary file formats to the OME data model, generating OME-TIFF as a potential output file. [...]
Back to: Microscopy File Formats Bioimaging File Formats explained The smallest piece of information underlying a computer is the distinction of two states (on or off), which can be represented as a binary digit (bit) with values 1 or 0. To store more complex information, more bits are combined. E.g., 8 [...]
Metadata is often referred to as "data about data". It describes properties associated with the experiment that has led to the pixel image including all information to fully understand what was imaged and how the image was generated.Technical metadataThis metadata includes information on the hardware that was used to acquire an image and which settings [...]
How is data and metadata structured in bioimaging? To provide a comprehensive overview of the most important technical terms and concepts with respect to metadata, the I3D:bio team created a poster that combines a glossary on terms with the conceptual relationships between different terms. This poster is also presented in a recorded poster talk by [...]
