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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 130 image file formats supported, including all major microscope formats.

Import

Organize

View

Analyze

Export


Getting Started

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.

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 130 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.

Use the OMERO.insight client to browse and import your images (version 4.4) Import images using the command-line interface (version 4.4)

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]

Connecting to OMERO using OMERO.insight on Mac and Windows Using Projects and Datasets in OMERO.insight Using Projects and Datasets in OMERO.web
Annotating data with Tags, Ratings, Files etc in OMERO.insight Use the OMERO.editor to add protocol and experimental details to your data An introduction to the group permissions system in OMERO.insight
See how tags can be shared within a collaborative group (OMERO.insight) Overview of collaborative features in OMERO.web Individual images can be 'shared' for a specified duration with chosen users using the web client's 'Share' feature.
Annotating data in OMERO.web

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.

Browse and view images remotely on Windows and Mac Browse images and adjust rendering settings in OMERO.insight
Browse and view images in the OMERO.web app View Acquisition metadata alongside your images

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.

Draw ROIs, in 2D, or across 3D or 4D. Measure distances, sizes, pixel intensity of ROIs and export to an Excel spreadsheet.
An intro to the OMERO Scripting Service The script-writing workflow
An example of using OMERO.scripts to add image processing and analysis functionality to the OMERO server.

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: 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.

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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