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Biological Imaging Data Processing for Data Scientists



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.



Balaji Ramalingam, University of Dundee

Jean-Marie Burel, University of Dundee

Petr Walczysko, University of Dundee


Audience and Prerequisites

  • Life scientists with programming skills, bioinformaticians and image analysts.
  • Anybody interested in using Jupyter and OMERO
  • Attendance to the introductory course on Biological Image Data Management for Life Scientists is recommended.
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals.


Syllabus, Tools and Resources

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


Learning Objectives

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



Book Here

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