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Fri 8 Dec 2017
09:30 - 17:00

Venue: Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Provided by: Bioinformatics


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Biological Imaging Data Processing for Data Scientists

Fri 8 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 transition from manual data processing to automated processing workflows. We will introduce how to write applications against the OMERO API, how to integrate a variety of processing tools with OMERO and how to automatically generate output ready for publication.

This course is organized alongside a one day course on Biological Imaging Data Management for Life 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
  • Life scientists with programming skills, bioinformaticians and image analysts.
  • Anybody interested in using Jupyter and OMERO
  • 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

Attendance to the introductory course on Biological Image Data Management for Life Scientists is recommended.


Number of sessions: 1

# Date Time Venue Trainers
1 Fri 8 Dec 2017   09:30 - 17:00 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Balaji Ramalingam,  Jean-Marie Burel,  Petr Walczysko
Topics covered

Bioinformatics, Biological imaging, Data management


After this course you should be able to:

  • Prepare reusable workflows for streamlined investigations
  • Familiarise yourself with the OMERO eco-system.
  • Write applications against the OMERO API and package them for use by others where appropriate.
  • Use a variety of open-source and proprietary processing tools with your OMERO data
  • Prepare analytical results for publication

During this course you will learn about:

  • Getting started with Jupyter
  • Retrieving image data and metadata using an API
  • Integrating 3rd party tools to process your data in OMERO: R, ImageJ, CellProfiler
  • Saving generated analytical results back to OMERO
  • Managing and sharing data at scale
  • Creating programmatically figures ready for publication/presentation

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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