[ome-devel] [ome-users] Light-sheet data publication with OMERO.

[Christophe TREFOIS]

Hi Emil,

Congratulations also from our side :)

Based on our chat, I will formalise a couple of questions that might benefit the whole community, especially about the process that you took to get this nice tool ready.

- How did you save the layers? Did you use different images, or channels or something more internal to OMERO?
- How do you make the dataset public? I assume people are working with images in private setting for quite some time and then at the date of publication, the images are made publically available.
- Is the code of the webclient available on some public repo?
- Did you carry out any modifications on the server side?
- Will you guarantee availability of data over couple of years? 10? more?

Kind regards,

—
Christophe

Dr Christophe Trefois, Dipl.-Ing.
Technical Specialist / Post-Doc

UNIVERSITÉ DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEIDINCE
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On 03 Apr 2015, at 15:46, Jason Swedlow (Staff) <j.r.swedlow at dundee.ac.uk<mailto:j.r.swedlow at dundee.ac.uk>> wrote:

Hi Emil

Thanks for this update, and congrats on the publication of your paper and this data set.  It’s a great example of the kind of thing we want to enable with OMERO and Bio-Formats.

Several people have asked us to document the set-up and configuration of OMERO as a public data sharing repository.  We’ll definitely try to capture your experience, as well as several others in this doc and get this included in the 5.1.1 release.

Congrats again on this great work.

Cheers,

Jason



On 31/03/2015 15:39, "Emil Rozbicki (Staff)" <e.j.rozbicki at dundee.ac.uk<mailto:e.j.rozbicki at dundee.ac.uk>> wrote:

Dear OME developers,

I would like to share with you our latest achivement which couldn't have happened without your effort. We have succesfully published a light-sheet microscopy dataset together with the analysis results using OMERO as a publication platform. The dataset is avaiable here: http://omero-cjw.lifesci.dundee.ac.uk/10.15132.10000100/ and is published alongside Nature Cell Biology manuscipt http://dx.doi.org/10.1038/ncb3138.

Some technical details:
The original dataset has almost 100 Gigapixels while the OMERO available image holds half of it. The OMERO image contains one channel with the microscopy data and further 18 channels with the analysis results. The image served by OMERO is around 50GB, including all analysis results. The dataset is downloadable from the website with substantially compressed analysis outcomes taking it all down to 10GB.

I would like to thank you All for making the data publication so easy.

Regards,
Emil Rozbicki

The University of Dundee is a registered Scottish Charity, No: SC015096
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