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Thu 14 Jul 2016
09:30 - 17:00

Venue: Bioinformatics Training Room, Craik-Marshall Building

Provided by: Bioinformatics


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Biological Imaging Data Management for Life Scientists

Thu 14 Jul 2016


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.

OME has three components:

  • OME-TIFF, standardised file format and data model;
  • Bio-Formats, a software library for reading proprietary image file formats; and
  • OMERO, a software platform for image data management and analysis.

In this one day course, we will present the OMERO platform, and show how to import, organise, view, search, annotate and publish imaging data. Additionally, we will briefly introduce how to use a variety of analysis tools with OMERO.

This course is organized alongside a one day course on Biological Imaging Data Management for Facility Managers. More information on this event are available here.

This course will be delivered by members of the OMERO team. The OME project is supported by BBSRC and Wellcome Trust.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Target audience
  • Anyone wanting to use OMERO to organize, view, annotate and publish imaging data
  • Facility Managers wanting to train users
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Further details regarding eligibility criteria are available here
  • Further details regarding the charging policy are available here

Number of sessions: 1

# Date Time Venue Trainers
1 Thu 14 Jul 2016   09:30 - 17:00 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building map Colin Blackburn,  Balaji Ramalingam,  Gus Ferguson,  Colin Blackburn
Topics covered

Bioinformatics, Biological imaging, Data management


After this course you should be able to:

  • Import image and HCS data into OMERO
  • Organise, view and annotate data with Insight and webclient
  • Search for data within OMERO
  • Use OMERO web plugins to organise and publish data
  • Use a variety of open-source and proprietary analysis tools with your OMERO data

During this course you will learn about:

  • Getting started with OMERO
  • Importing and organizing your data
  • Viewing your data
  • Annotating and searching your data
  • Creating figures for publication and sharing
  • Using OMERO with image processing tools: ImageJ, Icy, CellProfiler, Matlab, etc.

Presentations, demonstrations and practicals




A number of times per year

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