Two one-hour workshops on how to use OMERO held in Munsingen.
The Open Microscopy Environment (OME) is an open-source software project that develops tools that enable access, analysis, visualization, sharing and publication of biological image data. We support more than 150 image data formats across many imaging modalities including medical imaging, high-content screening and whole-slide imaging. We support and visualize multi-channel 3D timelapse images. OMERO, a component of OME, is a software platform for image data management and analysis which was presented in this course. Import, organisation, viewing, searching, annotation and publishing of imaging data with OMERO were shown.
The workshop concentrates on basics of OMERO and did not assume any programming skills.
We also showed hints about how to transition from manual data processing to automated processing workflows using applications against the OMERO API, how to integrate a variety of processing tools with OMERO such as CellProfiler, Orbit, ImageJ, R and how to automatically generate output ready for publication.