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Open Microscopy Environment Remote Objects - OMERO

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OMERO is an open source client/server system written in Java for visualizing, managing, and annotating microscope images and metadata. The OMERO API allows clients to be written in Java, Python, C++ or MATLAB. The OMERO platform includes a Java client OMERO.insight, a Python-based web client OMERO.web, a Command Line Interface which uses Python, and a Java ImageJ plugin. OMERO also supports a scripting service which allows Python scripts to be run on the server and called from any of the other clients. OMERO is a data management software that allows storing, organizing, and annotating bioimaging/microscopy data. OMERO has become one of the best-known systems for bioimage data management in the bioimaging community.

Features:

  • Upload: OMERO stores your images, using Bio-Formats to read metadata and pixel data on import. More than 140 file formats are supported

  • Managing: View acquisition metadata, add your own annotations and use them to filter your data

  • Sharing: Share your images and collaborate with colleagues using the permissions system

  • Viewing: Use OMERO’s 5-dimensional image viewers to work with your data from anywhere over the internet

  • Analyze: Analysis apps can access images on OMERO and save results back to the server. OMERO.scripts run on the server itself and can be launched from the clients

  • Publish and export: Publish your data straight from the server with an embedded viewer or link to a separate app. Use the permissions system to regulate access to this public data. Download original image files or export as OME-TIFF

OMERO at UFZ

Within NFDI4BIOIMAGE an image data repository based on OMERO will be implemented at the UFZ. Together with the departments phyDiv, ETOX and iCyt platform we establish workflows for data acquisition by high-content, high-throughput microscopes, storage of image data and metadata in the repository and usage of the (meta)data in data analytic workflows based on KNIME and other machine learning tool chains. An OMERO instance at UFZ is fully operative, and it is accessible at this link.

About OMERO

OMERO itself has a very detailed guide as well as a good documentation for the latest version.