OMERO guide

The OMERO guide offers step-by-step instructions on how to use components of the OMERO platform.

To learn more about OMERO, we recommend that you first visit the Open Microscopy Environment Website.

You can also watch videos of OMERO features or workshop recordings on the Open Microscopy Environment YouTube channel.

Getting started

OMERO walkthrough example presents a step-by-step example of a typical OMERO user workflow from import to figure creation.

OMERO walkthrough for facility managers gives a typical workflow of a facility manager helping and guiding their users to use the local OMERO ecosystem.


The OMERO guide is divided into several parts:

General concepts covers how to get started, import, manage data, users, groups and run server-side OMERO scripts.

OMERO.web extensions to view data includes instructions for installing Web plugins and how to use those extensions points e.g. OMERO.iviewer, OMERO.figure, OMERO.parade.

Add-ons for OMERO includes instructions for installing plugins for OMERO.insight and the Command Line Interface and how to use those extension points.

OMERO Application Programming Interfaces allows clients to be written in Java, Python, R, C++ or MATLAB. This section includes installation instructions and an exhaustive list of examples.

External Software and OMERO introduces how to analyze data using third party tools e.g. Fiji, CellProfiler, ilastik.

Prepare an OMERO server for training

Prepare an OMERO server for training presents a step-by-step example of a setup needed to get a training server similar to the one used by the OME Team.

All the guides are hosted on GitHub. If you wish to create a new guide, check the instructions on How to write a guide.

Click on the icon to go the relevant part of the guide.

fiji ilastik cellprofiler tm orbit qupath

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