OME Stories
OMERO as image data management for a changing community
Oliver Müller
Institute for Molecular Cell Biology, Saarland University, Germany
“As in most academic institutions, bachelor, master or PhD students regularly leave our lab after their project is finished. To avoid loose collections of lab book pages and piles of DVDs that are hard to manage by the supervisors, we have started to standardise the way data, especially image data is managed: we are using OMERO (at differing levels since 2007).
Each member of our institute is obliged to organise image data, measurement protocols as well as results using the OMERO client-server architecture. As a result, the period of vocational adjustment of new group members could be successfully reduced.
We hope, that the option to share data (within the 4.2 OMERO release) will foster collaborative work and thus lead to an improved workflow.”
Integrate OMERO into your data management system
Chris Tomlinson
Centre for Integrated Systems Biology, Imperial College, UK
“We have been operational at Imperial College with OMERO since April and had over 100GB of image data stored within the first few weeks and about 20 different users. We will be spreading the word around the university more in the coming weeks and months and so far all is working very well.
In addition to OMERO's standard use, we have integrated it into our data management system as a whole so that sample preparation steps can be directly linked to images and image data sets (and also to other data modalities). The application that does this integration is called XperimentR and demonstrates quite well the use of the OMERO API.”
Using OME software across institutions
Jerome Avondo
John Innes Centre, UK
“We currently have two OMERO systems up, one at the University of East Anglia, Norwich, UK. And one at the John Innes Centre, Norwich, UK. The first runs on CentOS and the second on Red Hat. We use these two server in order to facilitate data transfers as our lab is a collaboration between the two entities.
We also use (daily) the Bio-Formats library to convert microscope specific formats to OME-TIFF files, to facilitate getting data into our various analysis software.
We plan on now investigating the use of OMERO as the backbone to facilitate image processing for large batches of data. We will investigate using work-flow tools such as Taverna in order to create processing pipelines, which will then interact with OMERO for getting data out and in, and recording processing metadata.”
Jerome was instrumental in getting the OMERO system installed at these institutions. We were able to provide some pointers and help with installation via our user mail lists and forums.
Using Bio-Formats within an open-source application
Daniel James White
Max Planck Institute of Molecular Cell Biology and Genetics, Germany
“We in the Fiji dev team are very happy that Bio-Formats has been very successfully included in the Fiji distro of ImageJ, and we are really happy that the flow of information when finding and fixing bugs in Bio-Formats is fast and functional.…”
The Bio-Formats plugins allow any Fiji user to open any of the proprietary file formats supported by Bio-Formats. As Bio-Formats is upgraded the users get access to new formats and improved support for existing formats via the built-in Fiji Updater. Fiji developers can use the Bio-Formats API to gain largely automatic support for all of the many supported formats.
Commercial Development for the OMERO Platform
Kees Machielsen
DAX Archiving Solutions, The Netherlands
“We have developed an OMERO Storage Manager that enables users to manage their storage within the OMERO environment. We have installed it at Institut Pasteur in Paris for evaluation.”
DAX have developed a commercial product that will sit between an OMERO server and the disk storage to provide access to an archiving system. Further information
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