Services offered by Glencoe Software

Licensing

OMERO and Bio-Formats are open source, freely available software tools, licensed for use and distribution through the GNU General Public License Version 3 (GPL). Glencoe Software provides commercial licenses for both OMERO and Bio-Formats. If you would like to use either in a commercially licensed package, you must contact sales at glenceosoftware.com, for a commercial license.

New file formats and imaging modalities

OMERO currently supports several dozen file formats, thanks to the Bio-Formats software. Each supported format can be imported into the server, and accessed by any OMERO client.

However, new formats frequently appear, and the open-source solution may not yet provide one you need. Glencoe Software offers you the chance to sponsor the support for a particular file format to more quickly gain access to your data. In the more extreme case, Glencoe Software can also provide a closed-source solution. Please contact us for details.

But more than just new file formats, entire imaging domains may not be represented in the open source software, which grew out of light-microscopy labs. The OMERO platform, however, is a base for managing and analyzing any imaging data. In concert with field specialists, OMERO can be extended into these other imaging modalities from flow cytometry to mass spectrometry.

Server customization

Where needed, Glencoe Software can provide builds of the OMERO software with customizations for your site or application.

Security Integration. No matter what your security backbone — LDAP, PAM, etc. — the OMERO server's security system can be integrated with your existing framework. The LDAP plugin, for example, currently transparently creates the OMERO "experimenter" on an LDAP user's first login. Similarly, users' OMERO sessions can be tied to some session-concept in your framework, allowing for temporary logins, single-sign on semantics, or other security features.

Database extensions. Though the OME project strives to provide a robust and generally useful data model, it is not uncommon for research facilities or application developers to have additional modelling needs. Rather than developing, deploying, and maintaining a second data store, a database extension with the OMERO framework may be more cost-efficient.

Specialized indexing and search. Whether your own database extension or a unique facet of the existing model, a "search bridge" can be developed for your site, which indexes data and provides it in a simple, Google-style interface:

Optimized queries. While retrieving data through the OMERO API is both fast and flexible, eventually the needs of individual applications will require several method calls before all the needed metadata has been retrieved. Each method call incurs both network and database overhead. Instead, single queries can be written which acquire a much larger data graph in far less overall time. These can be parameterized for wide-spread use, and stored either in the database or in a text file for simplified updating.

Integrated backups. A generic backup solution is difficult if not impossible, and so is not included in the open source solution. Instead, a basic backup tutorial is provided, and the individual system administrator must tailor a solution. If, however, you'd like a custom backup solution built for you, taking into account your storage solution, including space, archiving schedules, group quotas, and various other factors, please contact us.

Client customization

Glencoe Software can provide customised versions of OMERO client applications, like OMERO.importer and OMERO.insight. Whether you need an integrated import, data-specific views, or simply themed clients to work with your software,

Metadata support. Though your file format may be supported in OMERO, if the data and metadata are not readibly available from the clients, they are little value for your users. New panels specifically tailored to your workflow can easily be integrated as agents.

Advanced visualization. Screening applications and other high-content or high-throughput tasks can be significantly facilitated by the correct visualization. Heat-maps and other views can be delevoped as extensions to the OMERO clients.

Consulting and support contracts

Glencoe Software employees have a range of expertise in developing and deploying large-scale systems for the management and visualization of scientific data.

Enterprise-level hardware. Purchasing, installing, deploying, and making full use of your storage and computing resources can be time-consuming and error-prone. A lab or institute is most likely to make large-scale purchases for the first time at the beginning of a large project, a time when serious mistakes are most hazardous. Let our experienced staff outline a solution for your computing needs and get your system administrators up to speed.

Hosting solutions. If, instead, you would prefer to allow Glencoe Software to deploy and maintain the hardware remotely, a hosting plan can be created to match your needs.

Server architecture. The switch to a client/server model can often be a complicated one. Though the collaborative and performance benefits of having a centralized server are enormous, users and developers alike can find it difficult to step out of the traditional standalone, desktop role. Our architects can help you plan the creation of new, asynchronous, distributed services which can make full use of your computing capacity.

Analysis integration. If your facility is involved in the creation of analysis routines, Glencoe Software can provide the necessary glue-code to integrate your application with the OMERO server. One example of such a binding is the Matlab interface developed and maintained in the open-source project. As with new file formats, options are available for sponsoring new application interfaces in the open-source code base or for producing a new proprietary one.

Support. In addition to project-based consulting, support contracts are available for guaranteed access to OMERO developers and extended documentation examples.