OMERO Documentation

The following are links to the open source OMERO user guides. Most of the open source help guides apply to the version of OMERO Plus we are using here at HMS. However, there are some important differences, especially in the area of downloading and installing the software.

Please note that most of the instructions for how to download and install OMERO.insight and other client software DO NOT APPLY to our environment.

The open source instructions only are intended for open source installations of OMERO. At HMS we have a custom version of OMERO Plus. Use the instructions for downloading and installing OMERO.insight and other client software found on the Software section of this website. Accessing this page requires logging in with your Harvard Key

How to get and install OMERO.insight

  1. First go to and make sure you have the latest Java 8 installed on your computer. Java 9 is not supported.
  2. Go to the IMC Download page and select and download the appropriate installer for your operating system. You will need a Havard Key to access this page.
  3. Extract OMERO.insight and move to a convenient location on your computer. For Macs this is usually the Applications folder. On Windows it usually Program Files. 
  4. Open OMERO.insight. On Macs you will have to go to the System Preference Security and Privacy settings and allow OMERO.insight to run. If you have never run OMERO.insight before you will have to enter the server address. See the online help for instructions on how to add the address for the HMS OMERO server:

Open Source OMERO Help Guides from

Using OMERO with the O2

HMS OMERO has been designed to be used with the O2, the HMS Research Computing HPC cluster. Researchers may access and perform various functions on their microscope images using the command line OMERO tools installed on O2. Using the O2 HPC cluster with OMERO is potentially very powerful and convenient. For example, importing very large datasets with more than 2,000 images can be efficiently performed on O2 using the command line importer (CLI).

Caution!: Using the O2 cluster to access OMERO server can potentially overload the server and adversely affect the ability of other users to access the system. Therefore we ask that users interested in using O2 for processing and managing their images contact the Image Management Core to discuss your interest in this capability.