[ome-devel] extending OMERO

[Stephen Taylor]

Hi Ilan,

I would be very interested to see some example data. Is there any online examples you would recommend?

Kind regards,

Steve



From: Ilan Davis
Sent: 24 April 2014 06:41
To: Stephen Taylor; Douglas Russell
Cc: ome-devel at lists.openmicroscopy.org.uk; Roger Noble (roger at coritsu.com); Shankar Srinivas; Richard Parton; Ian Dobbie
Subject: Re: [ome-devel] extending OMERO

Hi Steve
I am wondering whether the PivotViewer can also be modified to visualise the huge data sets generated by Light Sheet microscopy - generating a very large number of Z sections - potentially many angles and also very many time
points. Conventional viewers are quite poor at dealing with such data and in addition there are quite clever algorithms required to visualise such data smoothly by merging multiple angles and visualising tomograms.
Many thanks
regards
Ilan

____________________________________________________________________________
Prof. Ilan Davis   ilan.davis at bioch.ox.ac.uk<mailto:ilan.davis at bioch.ox.ac.uk>   Web site: http://www.ilandavis.com<http://www.ilandavis.com/>
Department of Biochemistry, The University of Oxford, South Parks Road, OXFORD OX1 3QU, UK
Direct Office No: (44) (0)1865 613265    Lab: 613271 / 613272   Fax: 613340
Postdoctral lab manager: Dr Thomas Germe 613271 / 613272  Thomas.Germe at bioch.ox.ac.uk<mailto:Thomas.Germe at bioch.ox.ac.uk>
PA:  Sian Annely 613218 sian.annely at bioch.ox.ac.uk<mailto:sian.annely at bioch.ox.ac.uk>
____________________________________________________________________________






On 23 Apr 2014, at 17:26, Stephen Taylor <stephen.taylor at imm.ox.ac.uk<mailto:stephen.taylor at imm.ox.ac.uk>> wrote:


Hi,

We are planning to extend OMERO to be able to support our zoomable image and query interface called PivotViewer (for details see http://www.cbrg.ox.ac.uk/data/pivotviewer/intro.shtml) or to view it in action, see the YouTube movie (https://www.youtube.com/watch?v=BvDOPpRo7KM).

We have 3 main goals:

1) Visualise OMERO projects by :
          i)  Generating indices for PivotViewer by doing an export of metadata (possible from the HDF5 tables) and images from the OMERO database.
          ii) Exporting the images + metadata on the fly.
2) Use the results of filtering operations to run OMERO.scripts and see the results in PivotViewer.
3) Use the results of filtering operations to be able to annotate back to the OMERO database. So for example, I might choose a subset of images that I think are badly stained and tag them as 'stained=bad' or similar.

I am trying to pull together enough technical information to define how much work would be required to do this as part of a grant application. Would anyone on this list be able to help?

Also, if any developers are interested in collaborating on this project please let me know!

Kind regards and thanks,

Steve
=======================================
Head of Computational Biology Research Group
Weatherall Institute of Molecular Medicine
University of Oxford
www.cbrg.ox.ac.uk<http://www.cbrg.ox.ac.uk>



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