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Thu 7 Dec 2017
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 7 Dec 2017


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 processing tools with OMERO.

This course is organized alongside a one day course on Biological Imaging Data Processing for Data Scientists. 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
  • Please be aware that these courses are only free for University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here

Number of sessions: 1

# Date Time Venue Trainers
1 Thu 7 Dec 2017   09:30 - 17:00 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building map Balaji Ramalingam,  Jean-Marie Burel,  Petr Walczysko
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 webclient
  • Search for data within OMERO
  • Use OMERO web plugins to organise, view and publish data
  • Use a variety of open-source and proprietary processing 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, orbit, etc.
  • Managing and sharing data

Presentations, demonstrations and practicals

Registration fees
  • Free for University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here



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