1- Getting started

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OMERO is a powerful microscopy images data management solution, handling all your images in a secure central repository. You can view, organize, analyze and share your data from anywhere you have internet access.

It works with your images from a desktop app (Windows, Mac or Linux), from the web or from 3rd party software. Over 150 image file formats supported, including all major microscope formats.


Omero.web is the web interface to interact with Omero server at omero-prod.icm-institute.org using any web browser, all you need is your icm login information.

Very Important: After your first connexion, and only after the first one, you will be logged in to a common group called ‘omero_users’. Hence,  you must notify the helpdesk omero-helpdesk about your first connexion. Helpdesk will create and configure your ‘team group‘ (if it does not exist yet) and attach your personal account to this group. You will be invited to reconnect in order to log your default group. The scenario is illustrated here.

Within Omero-web you can organize and annotate your projects, view, share and filter your image data. The interface can be upgraded with many web-apps developed separately to deal with Omero api, for example: Omero.iviewer, Omero.figures, FPBioimage…

Please see this help page for more details.



OMERO stores image data on a central server. You can use the OMERO.insight client to upload, view and download data from any personal computer.

According to your operating system, download OMERO.insight from links below:

Installation instructions can be found here. Note that Java version 1.7 or higher must be installed.

General data workflows:

Image data acquired by any research team member, at ICM microscopy image facilities, can be uploaded directly to Omero server (at the datalake storage) using Omero Insight client. Then, the image organisation, annotation and analysis can be performed at the team lab or from any other site using web connexion.


All Omero ‘s basic features are described below:

  • Importing Data into Omero is only possible with OMERO.insight.
  • Viewing Data using OMERO.insight and OMERO.web are essentially the same in both clients.
  • Managing Data in OMERO.web and OMERO.insight to organize and annotate Projects/Datasets/Images using tags and key/value.
  • Sharing Data with any group member and  user not in group is possible.
  • Searching data, additionally to image filters. You can search any ‘keyword'(s) in the imported metadata or attached files.
  • Exporting Data from Omero repository in the original format or others.
Advanced data workflows:
    • Draw Regions of Interest (ROIs) and perform some basic analysis using the measurement tool in OMERO.insight.
    • Draw Regions of Interest (ROIs) and perform some basic analysis using the OMERO.iviewer.
    • URLs for Linking to data. A simple way to access data Projects/Datasets/Images.
    • Managing Omero groups. (for group-owner only). To administrate the group members and data organisation.
    • OMERO comes with some scripts pre-installed, to add functionality such as the Populate Metadata (under the “‘import_scripts’ item in the menu) and “‘utility scripts”’. Custom scripts can be installed on the server by the system administrator so they are available to all users. For details see the scripts documentation page.