OMERO Overview and CLI User Documentation

Introduction

OME Remote Objects (OMERO) is a modern client-server software platform for visualizing, managing, and annotating scientific image data. OMERO lets you import and archive your images, annotate and tag them, record your experimental protocols, and export images in a number of formats. It also allows you to collaborate with colleagues anywhere in the world by creating user groups with different permission levels. OMERO consists of a Java server, several Java client applications, as well as Python and C++ bindings and a Django-based web application.

The OMERO clients are cross-platform. To run on your computer they require Java 1.8 or higher to be installed. This can easily be installed from https://java.com/ if it is not already included in your OS. The OMERO.insight client gets all of its information from a remote OMERO.server — the location of which is specified at login. Since this connection utilises a standard network connection, the client can be run anytime the user is connected to the internet.

The OMERO Platform

This documentation is for the OMERO 5 Platform. This version is designed to improve our handling of complex multidimensional datasets. It allows you to upload your files in their original format, preserving file names and any nested directory structure in the server repository. For more technical information, please refer to the Developer Documentation. You can read about the development of OMERO in the OMERO version history and the latest user-facing changes in What’s new for OMERO 5.4 for users.

Additional resources

  • OMERO for scientists introduces OMERO for new users, while the feature pages provide an overview of the platform features by type, including community developed apps and integrations which could help OMERO meet your research needs more fully.
  • You can try out OMERO without committing to installing your own server by applying for an account on our demo server.
  • Workflow-based user assistance guides are provided on our help website.
  • The OME YouTube channel features tutorials and presentations.
  • As OMERO is an open source project with developers and users in many countries, connecting to the community can provide you with a wealth of experience to draw on for help and advice.
  • Our popular OMERO.web app, OMERO.figure, has its own mini website at figure.openmicroscopy.org where you can find demo movies and a full release history.