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

Thu Apr 9 10:04:56 BST 2015

Hi Christophe,

Congratulations also from our side :)
Thanks a lot.

- How did you save the layers? Did you use different images, or channels or something more internal to OMERO?
The extra layers with the data analysis results were added as channels. We have used a pattern file (https://www.openmicroscopy.org/site/support/bio-formats5.1/formats/pattern-file.html) to group the '.tifs' together and import them to OMERO as a single image.

- 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.
At present this OMERO instance is only dedicated to data publication. I have followed the OME documentation on how to make the data public: http://www.openmicroscopy.org/site/support/omero5.1/developers/Web/PublicData.html. In our setup the public user does not own any of the data. The data is owned by other users that are also members of the "public-group". This is to make sure that I could make the data private prior the publication date. On the publication date I simply moved the data from a private group - private in a sense that the public users is not a member of it - to the "public-group", making the image publicly available - accessible by the public user.

- Is the code of the webclient available on some public repo?
Currently the code is not available anywhere beside the website itself :).

- Did you carry out any modifications on the server side?
We are running out-of-the-box OMERO 5.1 with no modifications. The only modifications happened to the Viewer. To be more precise I have stripped the Toolbox from the OMERO Viewer and added custom buttons to group the channels together. Some of the data analysis results are spread over 3 channels and they need to be toggled ON and OFF together.

- Will you guarantee availability of data over couple of years? 10? more?
We are obliged by the funding body of this project (BBSRC) to keep this data for 10 years, so it will be around for at least 10 years.

Cheers,

Emil

On 7 April 2015 at 14:35:15, Christophe TREFOIS (christophe.trefois at uni.lu) wrote:

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
Campus Belval | House of Biomedicine
7, avenue des Hauts-Fourneaux
L-4362 Esch-sur-Alzette
T: +352 46 66 44 6124
F: +352 46 66 44 6949  
http://www.uni.lu/lcsb

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On 03 Apr 2015, at 15:46, Jason Swedlow (Staff) <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> 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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