OME Presence at Innovation Portal Event
American Society for Cell Biology 48th Annual Meeting
Temp
The OME consortium develops several different software products for visualising, managing, and analysing microscope image data, all of which is freely available under the GNU public license.
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Data Management Applications
OME Server
Currently at revision 2.6.1, the OME server is a Perl-based system for visualising, managing, and analysing microscope images and metadata. It includes a web browser interface, a threshold segmentation and tracking application (called "findSpots"), a MatLab interface, support for VisBio, LDAP, Bio-Formats and much more.
If you are a new user then please read the comparison of the two servers to ensure you install the one that is right for you.
OMERO
OMERO is a java-based server/client system for visualising, managing, and annotating microscope images and metadata. It is a collection of seprate components that provide image visualisation, annotation, importing, archiving, protocol recording, and user administration.
If you are a new user then please read the comparison of the two servers to ensure you install the one that is right for you.
File Formats
Libaries - Bio-Formats
Developed by the Laboratory for Optical Computational Instrumentation group (LOCI), Bio-Formats is a standalone Java library for reading and writing popular microscopy file formats.
Specifications - OME-XML
OME partners at Dundee develop and maintain the OME-XML schemas that represent the data model.
Specifications - OME-TIFF
OME partners at LOCI have developed the OME-TIFF variant of the OME-XML file which is specifically designed for data acquisition and storage.
XSLT Transforms
There are some XSLT transforms available that operate on pre-July 2007 OME schema files.
Integration with third party tools
Matlab
There is a connector availabe to use the OME Server and Mathlab together. Install instructions and download details are available here
Excel
Two spreadsheets that can work with OME Server data are available. The can be downloaded from here
Java
There are Java APIs available to communicate with most of our software. See the developer documentation for the project you are interested in. It will be in the docs section.
ImageJ
You can use the bio-formats jar as a plugin for ImageJ. Simply download the jar file and follow the instructions here.
Standalone Applications
VisBio
OME partners LOCI are releasing VisBio, a standalone Java-based 5D image visualisation application. This tool supports complex image rendering and visualisation and also uploads and reads image to an original OME Server. We plan to have OMERO support in the next release.
