OME Remote Objects (OMERO) is a database for visualising, managing, and annotating scientific image data. You will use OMERO to import and archive your images, share data with your colleagues, annotate and tag image, and export images in a number of formats.
It also allows you to collaborate with colleagues anywhere in the world and to publically release the images used in your publications.
The general workflow is:
Acquire your images on the microscopes. If you use a consistent naming convention it will be easier to organise your images.
Keeping your data organised is a big challenge and OMERO has tools like tags and key-value pairs to help you out.
There's no one size-fits-all recipe for doing science, which is why OMERO doesn't force a particular workflow on you. This flexibility can be daunting at first so there are some example workflows that you might find helpful.