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About OMERO

What is OMERO?

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.

Import

Organize

View

Analyze

Publish

Export


Getting Started

Using OMERO as an image scientist

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.

Running OMERO for your institution

For System Administrators, there is an overview of the OMERO server here. Full documentation on how to install, configure and maintain your OMERO server is provided on the System Administrator documentation pages, where you will also find some recommendations for hardware and software requirements. We try to make the system as accessible as possible and you can always contact us for support but realistically, the system does require a level of familiarity and experience with running server applications. Alternatively, support packages are available from our commercial partner Glencoe Software.

All the documentation is also available as a PDF. You can download the latest version of OMERO from the downloads page.

Import

Browse the images on your local machine or file-system, select and add them to the import queue. OMERO uploads the images in their original format, stores them securely with all their metadata, and generates thumbnails for browsing. Bio-Formats (part of the OME project) allows OMERO to support over 140 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 the 'OMERO.insight' desktop application, or via the command line. OMERO also supports a 'Drop-box' on the server where any files copied to a specified directory are automatically imported.

Available user guides: Import images using OMERO.insight 5 Import images using the command line interface
Sysadmin guides: OMERO.dropbox In-place import Comparison of all import methods

Organize

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.

[1]

Available user guides: Managing data in OMERO.insight Sharing data in OMERO Using the search function
Optional extensions: OMERO.webtagging - extension for OMERO.web to automate and enhance tagging

View

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. OMERO also supports 'Big' images with viewers that allow you to pan and zoom in a 'Google maps' manner.

Available user guides: Viewing data with OMERO

Analyze

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.

Available user guides: Draw ROIs, measure distances, sizes, pixel intensity, and export to an Excel spreadsheet
OMERO Scripting Service: Use scripts to add functionality to your OMERO installation
Optional extensions: Partner projects linking OMERO to analysis tools including ImageJ and a particle tracker

Publish

With OMERO you can publish your raw data straight from the server. You can use URLs to link directly to the web-based image viewer in a manuscript or embed images directly into your website. You can control the level of access members of the public have to your data, for example by restricting downloads, and use the permissions system to allow or disallow comments, ratings etc.

Available user guides: Publish your data
Sysadmin guides: Customize your OMERO clients Configure your OMERO installation to host public data

Export

Export your images together with their metadata in their original file format or as ome.tiff files, supported by many other image analysis packages, or open them directly in ImageJ. Export data as a movie or as auto-generated figures ready for presentation.

Available user guides: Exporting images, including using scripts
Optional extensions: Use OMERO.figure for rapid smart figures with metadata
Export any image and its ROIs to ImageJ using the OMERO plugin, draw and save ROIs to OMERO from ImageJ OMERO.figure demo movies

Citation

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.

[1]
Dantas, et al., JCB, DOI: 10.1083/jcb.201012093
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