November 2019 OMERO users workshop

Registration: Contact the organiser directly

Organiser: workshop at the 29th New Zealand Conference on Microscopy

Location: University of Waikato, Hamilton, New Zealand

Date: 11th November 2019

Duration: One day workshop

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.

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, R and CellProfiler and how to programmatically generate output ready for publication.

This workshop was designed for researchers at all levels who work with data from digital microscopes or other imaging systems. The workshop included presentations and hands-on session. Prior knowledge in microscopy, scripting and data analysis was not required.

Any student/researcher dealing with scientific images was more than welcome to join this workshop.