Data Management (OMERO)

What is OMERO?

OMERO is an image data management system designed to support the vast amount of imaging data and provides easy ways of storing, accessing, displaying and working with that data.

From the microscope to publication, OMERO handles all your images in a secure central repository. You can view, organize, analyze and share your data from anywhere you have internet access. You can work with your images from a desktop app (Windows, Mac or Linux), from the web or from 3rd party softwares. 

Using the power of Bio-Formats, OMERO can read more than 150 image file formats, including all major microscope proprietary file formats. In particular, data from High Content Screening, time lapse imaging and digital pathology are supported, among other complex multidimensional image formats.

Accessing and managing your data is possible with all common browsers using the OMERO.web interface.
Creating figures for your publications is easy and straightforward with OMERO.figure, a web app that can access your images and their associated metadata from the database. Annotate your figures with automatic scale bars and clever labels, like toggled fluorescent channels or displayed time point…

OMERO at EPFL

Access to the EPFL-OMERO installation provided by the BIOP is available for all EPFL scientists. This was made possible thanks to the Open Science Fund program.

Authentication with gaspar credentials has been fully incorporated to the EPFL-OMERO installation, providing a straightforward and easy account setup for all EPFL users. At first logon, your account is automatically assigned to an OMERO group corresponding to your default EPFL accreditation. Please contact the BIOP team (Claire Stoffel) to be assigned to another group.

OMERO training

The BIOP offers training for the OMERO software most Tuesdays at 13h00. Inscription is mandatory and training takes place via ZOOM.

OMERO Training Registration

Why use it?

The Open Microscopy Environment aims to facilitate the handling of microscopy data as much as possible. For you this translates into the following features:

  • Organized and searchable database (find your data by experimenter, acquisition date, keywords…)
  • Easy access to data: Connect via the OMERO desktop app or from your web-browser
  • Fully integrated authentication: login with gaspar credentials
  • Easy sharing of data with colleagues and with the BIOP staff (single images, experiments, projects…)
  • Easy vector graphics figure creation for article publication, presentations..
  • Facilitated and safe transfer from the microscope to the server.
  • Facturing of the server space on the TB basis 
  • Connection with analysis softwares: Use ImageJ/Fiji, QuPath, scripts and other tools to run analysis on OMERO data and save results on the server. 
  • No more image exporting. Instead of exporting the images from the microscopy software and loose metadata, import the raw images to OMERO. 
  • Transparent metadata: Acquisition parameter like pixel-size, excitation wavelength, emission-wavelength etc. can be viewed at any time when browsing images
  • Open research: Publish raw data from a publication using OMERO.web public