OMERO clients overview¶
Most laboratories use a number of different imaging platforms and thus require tools to manage, visualize and analyze heterogeneous sets of image data recorded in a range of file formats. Ideally a single set of applications, running on a user’s laptop or workstation, could access all sets of data, and provide easy-to-use access to this data.
OMERO ships as a server application called OMERO.server and a series of client applications (known simply as clients): OMERO.web, OMERO.insight and OMERO.importer. All run on the major operating systems and provide image visualization, management, and annotation to users from remote locations. With a large number of OMERO.server installations worldwide, OMERO has been shown to be relatively easy to install and get running.
OMERO.insight and OMERO.importer are desktop applications written in Java and require Java 8 (or higher) to be installed on the user’s computer (this can easily be installed from https://java.com/ if it is not already included in your OS).
Our user assistance help website provides a series of workflow-based guides to performing common actions in the client applications, such as importing and viewing data, exporting images and using the measuring tool.
Our partners within the OME consortium are also producing new clients and modules for OMERO, integrating additional functionality, particularly for more complex image analysis. See the features pages for more details.
Features¶
Among many features, the noteworthy elements of the two main clients (OMERO.insight and OMERO.web) are:
DataManager, a traditional tree-based view of the data hierarchies in an OMERO.server. DataManager supports access to all image metadata, annotations, tags etc.
ImageViewer, for visualization of 5D images (space, channel, time). The ImageViewer makes use of the OMERO.server’s Rendering Engine, and provides high-performance viewing of multi-dimensional images on standard workstations (e.g. scrolling through space and time), without requiring installation of high-powered graphics cards. Most importantly, image viewing at remote locations is enabled. Image rendering settings are saved and chosen by user ID
Working Area, for viewing, annotating, and manipulating large sets of image data
user and group administration
OMERO.web¶
OMERO.web is a web-based client for users who wish to access their data in the browser. This offers a similar view to the OMERO.insight desktop client. Figures OMERO.web user interface and OMERO.web image viewer present the user interface. Developers can use the OMERO.web framework to build customized views.
OMERO.web user interface¶
OMERO.web image viewer¶
OMERO.web features almost all of the functionality of OMERO.insight barring import. A number of apps are available to add functionality to OMERO.web, such as OMERO.figure and OMERO.iviewer. See the main website for a list of released apps.
For more information and guides to using OMERO.web, see our help website.
OMERO.insight¶
Note
With the release of OMERO 5.3.0, the OMERO.insight desktop client has entered maintenance mode, meaning it will only be updated if a major bug is discovered. Instead, the OME team will be focusing on developing and extending the web clients.
OMERO.insight provides a number of tools for accessing and using data in an OMERO server. Figures OMERO.insight and OMERO.insight ImageViewer and Measurement Tool present the user interface. To find out more, see the OMERO.insight user guides.
OMERO.insight¶
OMERO.insight ImageViewer and Measurement Tool¶
The two main additional features of OMERO.insight which are not available as yet for OMERO.web are:
Measurement Tool, a sub-application of ImageViewer that enables size and intensity measurements of defined regions-of-interest (ROIs)
image import
Our user assistance help website features a number of workflow-based guides to importing, viewing, managing and exporting your data using OMERO.insight.
OMERO.importer¶
The OMERO.importer is part of the OMERO.insight client, but can also run as a stand-alone application. The OMERO.importer allows the import of proprietary image data files from a filesystem accessed from the user’s computer to a running OMERO server. This tool uses a standard file browser to select the image files for import into an OMERO server.
The tool uses Bio-Formats for translation of proprietary file formats in preparation for upload to an OMERO.server. Visit Supported Formats for a detailed list of supported formats.
OMERO.importer¶
OMERO.cli¶
The CLI is a set of Python-based system administration, deployment and advanced user tools. Most of commands work remotely so that the CLI can be used as a client against an OMERO server. See Command Line Interface as an OMERO client for further information.
