Tool assembly: OMERO
What is OMERO?
OMERO is a software platform for managing, sharing and analysing images data. OMERO supports over proprietary 150 file formats, including all major microscopy formats, medical images, digital pathology images, high content screening, etc. using Bio-Formats. Bio-Formats is a Java software tool for reading proprietary image data and metadata and writing image data using standardized open formats.
OMERO handles all your images in a secure central repository. Users can view, organize, analyze and share data from anywhere via the internet. Users can work with image data and metadata from a Desktop application, from the Web or from 3rd party tools e.g. Fiji.
OMERO stores image metadata in a relational database and offers a more flexible structure based on HDF5 to store for example, analytical results. This allows analytical results generated by 3rd party softwares e.g. CellProfiler, ilastik, etc. to be stored alongside the images.
Who is OMERO intended for?
OMERO is designed to be an institutional repository. It offers a secure central way for scientists, researchers and data stewards to handle their imaging data. All the image data from a facility can be securely stored and managed, using group permissions and user roles to allow controlled access tailored to your institution. From private repositories for sensitive data to hosting public data for your website and latest publications, the permissions model is designed to meet the range of researchers’ needs. OMERO is tried and tested in hundreds of institutions world-wide, with extensive installation and configuration documentation for system administrators and community support via dedicated mailing lists and forums.
The OMERO platform uses a Group/User permission system. The degree to which their data is available to other members of the group depends on the permissions settings for that group. Whenever a user logs on to an OMERO server, they are connected under one of their groups. All data they import and any work that is done is assigned to the current group, however the user can move their data into another group. Users require login credentials to access the system. OMERO also supports the use of an LDAP server.
OMERO is an open-source system designed to be extended and integrated with other tools. 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. A vast amount of documentation and code examples for scientists, developers and system administrators are available.
A demo server maintained by the OME team is also available for users wishing to try out, request an account.
Which tasks can be solved with OMERO?
The plaform can also be used to publish data either using public repository like Image Data Repository (IDR) or by enabling the public user within the OMERO installation in a given institution e.g. Liverpool CCI gallery.
OMERO is also used as a teaching platform by several institutions e.g. University of Dundee, Harvard Medical school.
General information about the OME ecosystem
Collection of presentations given over the years
Technical documentation for developers, system administrators
Collection of workflow describing to how use the system, with links to scripts and notebooks
YouTube channel with tutorials and presentations
Imaging Forum - discussions about imaging related topics
Relevant tools and resourcesSkip tool table
|Tool or resource||Description||Related pages||Registry|
|Bio-Formats||Bio-Formats is a software tool for reading and writing image data using standardized, open formats||Bioimaging data||Tool info Training|
|EMPIAR||Electron Microscopy Public Image Archive is a public resource for raw, 2D electron microscopy images. You can browse, upload and download the raw images used to build a 3D structure||Data publication Bioimaging data|
|Gene Expression Omnibus (GEO)||A repository of MIAME-compliant genomics data from arrays and high-throughput sequencing||Microbial biotechnology Data publication Documentation and metadata Data transfer Bioimaging data Toxicology data|
|Image Data Resource (IDR)||A repository of image datasets from scientific publications||Microbial biotechnology Data publication Documentation and metadata Data transfer Bioimaging data||Tool info Standards/Databases|
|OMERO||OMERO is an open-source client-server platform for managing, visualizing and analyzing microscopy images and associated metadata||Documentation and metadata Data Steward: research Data Steward: infrastructure Data storage Bioimaging data||Tool info Training|