Frequently Asked Questions

What is OMERO?

OMERO is a software platform for storing, managing, and sharing microscope images and metadata. 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. Work with your images from a desktop app (Windows, Mac or Linux), from the web or from 3rd party software. Over 140 image file formats supported, including all major microscope formats.

What happens to the images that are imported into OMERO?

OMERO makes an exact copy of the original files and metadata files recognized by BioFormats and stores them in the OMERO managed repository. The data is structured exactly as it was found when originally imported. As files are copied into the managed repository file hashes are computed and stored allowing for later verification that the files have not been altered. All subsequent interaction with the data is mediated by the OMERO system. The OMERO managed repository is stored on the HMS IT Isilon cluster.

What's the advantage of using OMERO over standard file storage?

OMERO is a far more effective way to manage large collections of microscope image data and metadata. Images can be tagged and annotated with OMERO without affecting the original file. The annotations and added metadata is stored in a high performance database and is searchable. Finding, sorting, and organizing images based on metadata is possible. On standard filesystems the typical approach is to encode metadata into filesystem paths and filenames. This forces people to use slow, inefficient filesystem tools to do basic sorting and searching.

What if OMERO.insight says I can't import a dataset or plate with more than 2,000 images?

OMERO.insight is not designed for importing datasets or plates with more than 2,000 images. Large imports can be performed with a command-line tool called the CLI, command line importer. The CLI is available on Orchestra. Using the CLI requires some familiarity with using the Orchestra compute cluster and the Linux command line environment. We can help you get started or we can do your imports for you. This is especially useful if you have lots of data you want to import into OMERO. We can design scripts to handle very large import tasks.

How to fix login problems with Chrome and Firefox

Occasionally Firefox and Chrome users cannot login to OMERO. In some cases users receive an error message that looks something like this: 

CSRF Error. You need to include valid CSRF tokens for any POST, PUT, PATCH or DELETE operations. You have to include CSRF token in the POST data or add the token to the HTTP header.

Other times the login fails and users cannot get beyond the public user login.