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.
Colin Blackburn, University of Dundee
Balaji Ramalingam, University of Dundee
Audience and Prerequisites
- 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.
Syllabus, Tools and Resources
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.
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