What is OMERO?
For info on how to get started, see the Getting Started guide (for users with access to an OMERO server) or try out our Demo Server. The clients page introduces the desktop and web applications you can use to work with OMERO, and workflow-based guides for many common tasks can be found on our user help website. For System Administrators, there is an overview of the OMERO server here. All the documentation is also available as a PDF. You can download the latest version of OMERO from the downloads page.
Browse the images on your local machine or file-system, select your images and add them to the import queue. OMERO uploads them, reads and saves the image metadata and generates thumbnails for browsing. For 'Big' images, a pyramid of zoom levels is generated in preparation for viewing. OMERO uses Bio-Formats (part of the OME project) to support over 120 image file formats, including all the major biological microscopy, HCS, tissue scanner and graphics formats. For a complete list of formats see Supported Formats. Import can be performed from a dedicated 'OMERO.importer' client, as well as from within the 'OMERO.insight' client. OMERO also supports import from the command-line as well as a 'Drop-box' on the server where any files copied to a specified directory are automatically imported.
|Use the OMERO.insight client to browse and import your images.||Use the dedicated OMERO.importer client to import your images||Import images using the command-line interface|
You can access your data in OMERO from any platform. Our client applications run on any OS (Windows, Mac or Linux) and the OMERO.web client runs in your browser. OMERO lets you organise your data how you want using 'Projects' and 'Datasets' to manage your images. You can create tags and tag groups to annotate images with key-words of your choice. OMERO also supports rating, comments, and file attachments. Once annotated, you can browse, filter or search your images by their annotations and export a table of tag-counts for a Dataset of images. Users of OMERO can be organised into groups, each with different permissions levels, allowing you to collaborate with your colleagues. You can share and annotate the data you want with the people you want.
In OMERO, you can view your images in multiple dimensions, scrolling through Z-sections and time-points. Turn channels on and off, change channel colours and adjust rendering settings. You can also copy and paste settings between images. Viewing images remotely in OMERO is fast, because you don't need to download the whole image to view it. OMERO simply renders the planes you want and sends the rendered image to the client. Even if you want to view a Z-projection: OMERO does the projection on the server and sends you the result. With the 4.3 release, OMERO supports 'Big' images with viewers that allow you to pan and zoom in a 'Google maps' manner.
|Browse and View Images remotely on Windows and Mac||Browse images and adjust rendering settings in Insight|
|Browse and view images in the OMERO.web app||View Acquisition metadata alongside your images|
In OMERO, you can draw regions of interest on your images and measure their dimensions and pixel intensities, exporting the data as a spread-sheet. OMERO supports Python scripting, allowing you to write analysis scripts that run on the server. These scripts can be launched from the OMERO.insight client allowing all users to access additional functionality on the server.
OMERO's open API allows clients written in Java, Python, C++ or Matlab to access image data and save analysis results back to the server, making OMERO a powerful platform for 3rd party analysis tools. OMERO includes a simple ImageJ plugin which allows ImageJ to access images on OMERO. For more info, please see the OMERO developer section.
Export your images together with their metadata as ome.tiff files, supported by many other image analysis packages or open directly in ImageJ. Export data as a movie or as auto-generated figures ready for presentation: see exporting images and using scripts to export figures.
|Export any image as OME-TIFF or open directly in ImageJ using the OMERO plugin.||Use OMERO to generate figures for presentation.|
The screenshots make use of data from the JCB DataViewer under the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License. For more information see Attribution.
- Dantas, et al., JCB, DOI: 10.1083/jcb.201012093