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 formatsinhibit sharing.For users, translating between data formats is imperfect, time-consuming andmust be performed repeatedly. Combined with the growing number of formats andadvancements in both data volume and complexity, translation is increasingly abottleneck.We will present recent work on a next-generation format that aims to enablea one-time conversion of datasets to a common format as well as theability to store them on highly-parallel object storage.We propose that such a next-generation format can revolutionize the sharing ofbioimaging data by expediting access and driving discovery.We imagine the samestrategy 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 will cover all of the main functions of OMERO. We will demonstrate data import, organisation, viewing, searching, annotation and publishing. After we cove the basics of OMERO, we will demonstrate manual data processing and automated processing workflows using a range of open source applications running alongside OMERO.We will demonstrate 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 will be run using public examples of multi-dimensional fluorescence, HCS and digital pathology data, hosted in the ImageDataResource (IDR), which is based on OMERO and other public resources.

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