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How to organize your image data with OMERO

December 7, 2023
Max-Planck-Institute for Evolutionary Biology
Europe/Berlin timezone

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During this training workshop, you will get all the information you need to get started in using the OMERO image database and webservice in your data collection, annotation, and analysis routines. In particular, these points will be covered:

  • Getting started: How to access OMERO
  • Importing image data into OMERO
  • Displaying images: The Viewer
  • Annotating images and datasets: Tags and Key-Value pairs
  • Creating publication ready figures with OMERO.figure
  • Exporting images
  • Loading images from OMERO in ImageJ and others
  • Bulk annotation workflow
Starts
Ends
Europe/Berlin
Max-Planck-Institute for Evolutionary Biology
Interim Lecture Hall
August Thienemann Strasse 2 24306 Plön

Collaborative Notepad:

https://s.gwdg.de/tMB3rr

Timetable

Day 1: Dec 7th 2023

Begin End Topic
9:00 9:15 Welcome and Introduction
9:15 10:30 Introduction and first steps
10:30 10:45 Break
10:45 11:15 Using the Viewer
11:15 12:00 Data Organization in OMERO
12:00 13:00 Lunch break
13:00 13:45 Annotation with Tags and Key-Value Pairs
13:45 14:00 Break
14:00 14:45 Bulk Annotations with forms and spreadsheets
14:45 15:15 Creating figures with OMERO
15:15 15:30 Connecting ImageJ and OMERO
15:30 16:00 Summary, Q&A, feedback

 

Required Software

If you bring your own laptop, please install the following software prior to the workshop:

  1. OMERO.Insight Desktop client: https://www.openmicroscopy.org/omero/downloads/
  2. Fiji: https://imagej.net/software/fiji/downloads
  3. OMERO-Fiji plugin: https://www.openmicroscopy.org/omero/downloads/ . Place the downloaded jar file into your Fiji plugins directory.
  4. A spreadsheet editor, such as MS Excel or LibreOffice Calc. Google sheets or Owncloud OnlyOffice also works.
  5. You will need to copy some datafiles from the mpistaff share. Please make sure you can access mpistaff.
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