<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.apple-tab-span
{mso-style-name:apple-tab-span;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-GB" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><font size="2" color="#1f497d" face="Calibri"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Ilan,<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">I would be very interested to see some example data. Is there any online examples you would recommend?<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>
<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"><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>
<div style="border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt">
<div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<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"">
Ilan Davis <br>
<b><span style="font-weight:bold">Sent:</span></b> 24 April 2014 06:41<br>
<b><span style="font-weight:bold">To:</span></b> Stephen Taylor; Douglas Russell<br>
<b><span style="font-weight:bold">Cc:</span></b> ome-devel@lists.openmicroscopy.org.uk; Roger Noble (roger@coritsu.com); Shankar Srinivas; Richard Parton; Ian Dobbie<br>
<b><span style="font-weight:bold">Subject:</span></b> Re: [ome-devel] extending OMERO<o:p></o:p></span></font></p>
</div>
</div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><o:p> </o:p></span></font></p>
<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>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">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<o:p></o:p></span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">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. <o:p></o:p></span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Many thanks<o:p></o:p></span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">regards<o:p></o:p></span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Ilan<o:p></o:p></span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><o:p> </o:p></span></font></p>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><font size="4" face="Helvetica"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif"">____________________________________________________________________________<br>
Prof. Ilan Davis <a href="mailto:ilan.davis@bioch.ox.ac.uk"><font color="black"><span style="color:black">ilan.davis@bioch.ox.ac.uk</span></font></a> Web site: <a href="http://www.ilandavis.com/"><font color="black"><span style="color:black">http://www.ilandavis.com</span></font></a><br>
Department of Biochemistry, The University of Oxford, South Parks Road, OXFORD OX1 3QU, UK<br>
Direct Office No: (44) (0)1865 613265 Lab: 613271 / 613272 Fax: 613340<br>
Postdoctral lab manager: Dr Thomas Germe 613271 / 613272 <a href="mailto:Thomas.Germe@bioch.ox.ac.uk"><font color="black"><span style="color:black">Thomas.Germe@bioch.ox.ac.uk</span></font></a><br>
PA: Sian Annely </span></font><font size="2" face="Calibri"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif"">613218 </span></font><u><font size="4" face="Helvetica"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif""><a href="mailto:sian.annely@bioch.ox.ac.uk">sian.annely@bioch.ox.ac.uk</a></span></font></u><font size="4" face="Helvetica"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif""><o:p></o:p></span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="4" color="black" face="Helvetica"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif";color:black">____________________________________________________________________________<o:p></o:p></span></font></p>
</div>
</div>
<div>
<p class="MsoNormal"><font size="4" color="black" face="Helvetica"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif";color:black"><o:p> </o:p></span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="4" color="black" face="Helvetica"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif";color:black"><o:p> </o:p></span></font></p>
</div>
</div>
<p class="MsoNormal"><font size="4" face="Helvetica"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif""><o:p> </o:p></span></font></p>
</div>
<p class="MsoNormal"><font size="4" face="Helvetica"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif""><o:p> </o:p></span></font></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><o:p> </o:p></span></font></p>
</div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><o:p> </o:p></span></font></p>
<div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">On 23 Apr 2014, at 17:26, Stephen Taylor <<a href="mailto:stephen.taylor@imm.ox.ac.uk">stephen.taylor@imm.ox.ac.uk</a>> wrote:<o:p></o:p></span></font></p>
</div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><br>
<br>
<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Hi,<br>
<br>
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">http://www.cbrg.ox.ac.uk/data/pivotviewer/intro.shtml</a>) or to view it in action, see the YouTube movie (<a href="https://www.youtube.com/watch?v=BvDOPpRo7KM">https://www.youtube.com/watch?v=BvDOPpRo7KM</a>).<br>
<br>
We have 3 main goals:<br>
<br>
1) Visualise OMERO projects by :<br>
<span class="apple-tab-span"> </span>i) Generating indices for PivotViewer by doing an export of metadata (possible from the HDF5 tables) and images from the OMERO database.<br>
<span class="apple-tab-span"> </span>ii) Exporting the images + metadata on the fly.<br>
2) Use the results of filtering operations to run OMERO.scripts and see the results in PivotViewer.<br>
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.<br>
<br>
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?
<br>
<br>
Also, if any developers are interested in collaborating on this project please let me know!<br>
<br>
Kind regards and thanks,<br>
<br>
Steve<br>
=======================================<br>
Head of Computational Biology Research Group <br>
Weatherall Institute of Molecular Medicine <br>
University of Oxford <br>
<a href="http://www.cbrg.ox.ac.uk">www.cbrg.ox.ac.uk</a> <br>
<br>
<br>
<br>
_______________________________________________<br>
ome-devel mailing list<br>
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><o:p></o:p></span></font></p>
</div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><o:p> </o:p></span></font></p>
</div>
</div>
</div>
</div>
</body>
</html>