Hi Jason,<div><br></div><div>Thank you for all the information, it has been very valuable to getting a base understanding of how OMERO can support EM.</div><div><br></div><div>I should be able to get more of an idea about the type of EM next week when I meet up with the researcher who asked the initial question.</div>
<div><br></div><div>Thanks again,</div><div>Kim<br><br><div class="gmail_quote">On 25 May 2012 09:20, Jason Swedlow <span dir="ltr"><<a href="mailto:j.r.swedlow@dundee.ac.uk" target="_blank">j.r.swedlow@dundee.ac.uk</a>></span> wrote:<br>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hi Kim-</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">As decribed in our recent paper on OMERO:</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><a href="http://www.openmicroscopy.org/site/about/publications" target="_blank">http://www.openmicroscopy.org/site/about/publications</a></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">We’ve used OMERO to hold EM data of a variety of types:</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><a href="http://emdb.openmicroscopy.org.uk/webemdb/" target="_blank">http://emdb.openmicroscopy.org.uk/webemdb/</a></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">I‘ve heard anecdotally of people using Columbus, Perkin-Elmer’s commercial version of OMERO, to manage EM data. Obviously, if Bio-Formats supports the data,
then OMERO (more or less) supports the data.</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">OMERO’s data model, as released doesn’t explicitly include support for tomographic tilt series. The data would go in, but the metadata will be wrong. A
proposed solution for this is here:</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><a href="http://www.openmicroscopy.org/site/support/file-formats/working-with-ome-xml/6d-7d-and-8d-storage" target="_blank">http://www.openmicroscopy.org/site/support/file-formats/working-with-ome-xml/6d-7d-and-8d-storage</a></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">The only other issue will be images from very large format cameras—OMERO, as released will treat these images as “Big Images”, calculate pyramids etc.</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">If you give us more detail about the specific type of electron microscopy you are interested in, we can probably tell you more about what you can and might
do.</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hope that helps.</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Cheers,</span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Jason</span></p>
<p class="MsoNormal"><a name="13781276fa021f9c__MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></a></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-users-bounces@lists.openmicroscopy.org.uk</a> [mailto:<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-users-bounces@lists.openmicroscopy.org.uk</a>]
<b>On Behalf Of </b>Kim Linton<br>
<b>Sent:</b> Monday, May 21, 2012 7:44 AM<br>
<b>To:</b> <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><br>
<b>Subject:</b> [ome-users] OMERO for Electron Microscopy</span></p><div><div class="h5">
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<p class="MsoNormal">Hi There,</p>
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<p class="MsoNormal">I am interested to see if anyone has used OMERO for Electron Microscopy?</p>
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<p class="MsoNormal">From what I can tell the file format are part of bioformats. </p>
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<p class="MsoNormal">Cheers,</p>
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<p class="MsoNormal">Kim<br clear="all">
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#888888">Kim Linton<br>
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Ph: <a href="tel:%2B61%203%2099020712" value="+61399020712" target="_blank">+61 3 99020712</a></span><span style="font-size:10.0pt;font-family:"Arial","sans-serif""></span></p>
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<div><div><div><div><div style="font-size:13px;margin-top:5px;margin-right:15px;margin-bottom:5px;margin-left:15px;padding-bottom:20px"><div><div style="color:rgb(0,0,0)"><font color="#888888">Kim Linton<br>Senior Research Systems Facilitator/Lead for the e-Research Portfolio<br>
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