November-December 2020 OME users workshops

Four 4-hour demos/workshops on "Next-generation file formats" and "OMERO" held remotely, organized by I2K virtual conference at HHMI Janelia.

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Organiser: I2K virtual conference at HHMI Janelia

Location: held remotely

Workshops: Next-generation file formats workshops and OMERO workshops

Dates: 30th November and 2nd December 2020

Duration: 4-hour workshops

Next-generation file formats: Bioimaging data, much like the subjects it illuminates, teems with diversity. But rather than driving evolution, differences in nomenclature and data formats inhibit sharing. For users, translating between data formats is imperfect, time-consuming andmust be performed repeatedly. Combined with the growing number of formats and advancements in both data volume and complexity, translation is increasingly a bottleneck. We presented recent work on a next-generation format that aims to enable a one-time conversion of datasets to a common format as well as the ability to store them on highly-parallel object storage. We propose that such a next-generation format can revolutionize the sharing of bioimaging data by expediting access and driving discovery. We imagine the same strategy is amenable to image repositories like the BioImage Archive or Image Data Resource, but also a large number of lab and institutional tools.

OMERO: This workshop covered all of the main functions of OMERO. We demonstrated data import, organisation, viewing, searching, annotation and publishing. After we covered the basics of OMERO, we demonstrated manual data processing and automated processing workflows using a range of open source applications running alongside OMERO. We demonstrated how to integrate a variety of processing tools with OMERO such as ImageJ/Fiji, ilastik, CellProfiler, and how to store analytical results alongside the image data for further analysis or, for example, publication. These hands-on practicals were run using public examples of multi-dimensional fluorescence, HCS and digital pathology data, hosted in the Image Data Resource (IDR), which is based on OMERO and other public resources.

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