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<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Douglas,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks, I’ll get back to you this!<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Kind regards,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Steve<o:p></o:p></span></font></p>
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<p class="MsoNormal"><b><font size="2" face="Tahoma"><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";font-weight:bold">From:</span></font></b><font size="2" face="Tahoma"><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
Douglas Russell [mailto:douglas.russell@bioch.ox.ac.uk] <br>
<b><span style="font-weight:bold">Sent:</span></b> 28 April 2014 09:22<br>
<b><span style="font-weight:bold">To:</span></b> Stephen Taylor<br>
<b><span style="font-weight:bold">Cc:</span></b> Simon Li; ome-devel@lists.openmicroscopy.org.uk; Roger Noble (roger@coritsu.com)<br>
<b><span style="font-weight:bold">Subject:</span></b> Re: [ome-devel] extending OMERO<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Hi Steve,<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">If you want to compile a list of things that you want to do with the API then I can prepare some examples and come up and show you them if you want? Especially with the
Python API I have quite a bit of experience now.<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Cheers,<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Douglas<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">On 25 April 2014 18:16, Stephen Taylor <<a href="mailto:stephen.taylor@imm.ox.ac.uk" target="_blank">stephen.taylor@imm.ox.ac.uk</a>> wrote:<o:p></o:p></span></font></p>
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<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Hi Simon,<o:p></o:p></span></font></p>
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<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">>As Jason pointed out in his email you should definitely be able to obtain all the information you need via the OMERO API, and we can certainly help you once you get started.<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">>Probably the easiest way to get started is to look at one of the language specific pages. Picking Python as an example, the code samples at ><a href="http://www.openmicroscopy.org/site/support/omero5/developers/Python.html#code-samples" target="_blank"><font color="black"><span style="color:windowtext;text-decoration:none">http://www.openmicroscopy.org/site/support/omero5/developers/Python.html#code-samples</span></font></a><o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">>cover the basics of connecting to OMERO, and retrieving/manipulating data. An intro to the full API is at
<a href="http://www.openmicroscopy.org/site/support/omero5/developers/Modules/Api.html" target="_blank">
<font color="black"><span style="color:windowtext;text-decoration:none">http://www.openmicroscopy.org/site/support/omero5/developers/Modules/Api.html</span></font></a><o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> <o:p></o:p></span></font></p>
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<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> We are planning to extend OMERO to be able to support our zoomable image and query interface called PivotViewer (for details see
<a href="http://www.cbrg.ox.ac.uk/data/pivotviewer/intro.shtml" target="_blank"><font color="black"><span style="color:windowtext;text-decoration:none">http://www.cbrg.ox.ac.uk/data/pivotviewer/intro.shtml</span></font></a>) or to view it in action, see the
YouTube movie (<a href="https://www.youtube.com/watch?v=BvDOPpRo7KM" target="_blank"><font color="black"><span style="color:windowtext;text-decoration:none">https://www.youtube.com/watch?v=BvDOPpRo7KM</span></font></a>).<o:p></o:p></span></font></p>
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<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> We have 3 main goals:<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> 1) Visualise OMERO projects by :<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> i) Generating indices for PivotViewer by doing an export of metadata (possible from the HDF5 tables) and images from the OMERO database.<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">>There are methods for listing images in Projects/Datasets/Screens, and for obtaining the raw images data and metadata. Are the HDF5 tables you refer to created using the OMERO.tables >API,
or are they created by yourself? If it's the latter there are API methods to retrieve the original HDF5 file (or any other type of file you want to store in OMERO).<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
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<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">OMERO.tables.
<o:p></o:p></span></font></p>
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<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> ii) Exporting the images + metadata on the fly.<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">>Could you expand on what do you mean by "export"? There are examples of rendering images on the fly on the code samples page, for more advanced usage you might want to look at the >source
code for OMERO.web.<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
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<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Ok. Currently we use static PNGs/JPGs and create a tiling pyramid which is read by the viewer, but it would be cool to generate these on the fly, caching the images of interest.<o:p></o:p></span></font></p>
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<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> 2) Use the results of filtering operations to run OMERO.scripts and see the results in PivotViewer.<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">>As you're probably already aware scripts are run asynchronously in a separate process. If you want something more responsive there may be other options.<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
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<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">No I didn’t know that. I’d be interested to hear about the other options...<o:p></o:p></span></font></p>
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<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> 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.<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
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<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">>This should be straightforward- once you've got a list of images (or any other OMERO objects) you can easily create a tag on them. It's also possible to attach more structured data to
?>an image.<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Ok. Sounds good. Is there a link where I can find more info about the different data structures available?<o:p></o:p></span></font></p>
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<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> 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?<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">>What kind of interaction do you want to see between OMERO and PivotViewer? Do you see it as a separate standalone application, or part of OMERO.web?
<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
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<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Ultimately it would be good to have as part of OMERO web but I think we have to get a bit more familiar with OMERO’s guts before we look at that. Doing it OMERO.web would be useful since
we could use the same authentication to secure collections, though I guess if both systems are using LDAP this might not be a problem. What other advantages do you think would be in using OMERO.web?<o:p></o:p></span></font></p>
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<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">>Do you need real-time updates- that >could be pretty challenging. However we've done (and are planning a lot more) work on integrating analysis tools into OMERO, so if you come across
>any issues don't hesitate to mention >them.<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
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<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">I think it would be standalone in the first instance and export the data (images and metadata) from OMERO incrementally and then index it on the file system.
<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Thanks for your help so far,<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Steve<o:p></o:p></span></font></p>
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<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> Also, if any developers are interested in collaborating on this project please let me know!<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> Kind regards and thanks,<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> Steve<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> =======================================<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> Head of Computational Biology Research Group Weatherall Institute of
<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> Molecular Medicine University of Oxford
<a href="http://www.cbrg.ox.ac.uk" target="_blank"><font color="black"><span style="color:windowtext;text-decoration:none">www.cbrg.ox.ac.uk</span></font></a><o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> _______________________________________________<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> ome-devel mailing list<o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> <a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">
<font color="black"><span style="color:windowtext;text-decoration:none">ome-devel@lists.openmicroscopy.org.uk</span></font></a><o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" target="_blank">
<font color="black"><span style="color:windowtext;text-decoration:none">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</span></font></a><o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> <o:p></o:p></span></font></p>
<p><font size="3" face="Times New Roman"><span style="font-size:12.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096<o:p></o:p></span></font></p>
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