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<div class="MsoNormal"><font class="Apple-style-span" face="Arial" size="5"><span class="Apple-style-span" style="font-size: 17px;"><div class="MsoNormal">Hi Christoph and Ingvar,</div><div class="MsoNormal"><br></div><div class="MsoNormal"> Many thanks for the useful discussions last week. Hope you both had a good Christmas. </div><div class="MsoNormal">Here is a bunch of notes I made afterwards. Please correct anything I have misunderstood. </div><div class="MsoNormal"><br></div><div class="MsoNormal">I am also sending this to the OME dev team as a basis for our discussions...</div><div class="MsoNormal"><br></div><div class="MsoNormal"> Cheers,</div><div class="MsoNormal"><br></div><div class="MsoNormal"> Will. </div><div class="MsoNormal"> </div><div class="MsoNormal"><br></div><div class="MsoNormal"><br></div><div class="MsoNormal">Goals:</div><div class="MsoNormal"><br></div><div class="MsoNormal">No plans to substantially change the EM-DB itself in the short term. Plan is to use OMERO for EM-maps, raw microscope images, and all other images in the workflow. EM-DB will remain the location of all publication, sample, experiment metadata etc. OMERO will hold limited EM imaging metadata equivalent to the LM metadata it currently supports. </div><div class="MsoNormal"><br></div><div class="MsoNormal">E.g. if scientists use OMERO for their EM images in their institutions, they should be able to automatically submit the whole workflow stack to the EM-DB, adding the necessary publication, sample and experimental metadata at the time of submission (not at the acquisition or processing stages). </div><div class="MsoNormal"><br></div><div class="MsoNormal"><br></div><div class="MsoNormal">OMERO viewers / API</div><div class="MsoNormal"><br></div><div class="MsoNormal">Want to be able to view a 3D-volume looking at a plane at any angle. Not just in the Z-axis. Also to project at any of these orientations. </div><div class="MsoNormal">Needs API changes. Required for maps and for segmentations. </div><div class="MsoNormal">E.g. see qsegment viewer of EMAN. </div><div class="MsoNormal"> </div><div class="MsoNormal"><br></div><div class="MsoNormal"><br></div><div class="MsoNormal">Web-client is important.</div><div class="MsoNormal"><br></div><div class="MsoNormal">-<span class="Apple-tab-span" style="white-space:pre"> </span>Users familiar with web-viewers: CCDB, EMDB etc. </div><div class="MsoNormal">-<span class="Apple-tab-span" style="white-space:pre"> </span>Many users on different platforms prefer not to download Java clients</div><div class="MsoNormal">-<span class="Apple-tab-span" style="white-space:pre"> </span>UI development on web is much improved with new libraries etc. </div><div class="MsoNormal"><br></div><div class="MsoNormal"><br></div><div class="MsoNormal">Open Astex Viewer</div><div class="MsoNormal"><br></div><div class="MsoNormal">-<span class="Apple-tab-span" style="white-space:pre"> </span>Stable code (in active use over 10 years)</div><div class="MsoNormal">-<span class="Apple-tab-span" style="white-space:pre"> </span>Runs as web applet (with Javascript controls) or as a Java viewer</div><div class="MsoNormal">-<span class="Apple-tab-span" style="white-space:pre"> </span>Needs some changes to make it suitable for EM-maps </div><div class="MsoNormal">-<span class="Apple-tab-span" style="white-space:pre"> </span>Burden of maintenance? Shouldn’t be very high. </div><div class="MsoNormal">-<span class="Apple-tab-span" style="white-space:pre"> </span>Do we make changes ourselves or ask Mike Hartshorn to implement them? <a href="mailto:openastexviewer@googlemail.com">openastexviewer@googlemail.com</a></div><div class="MsoNormal"><br></div><div class="MsoNormal"><br></div><div class="MsoNormal">ROIs / masks</div><div class="MsoNormal"><br></div><div class="MsoNormal">Need 3D masks:</div><div class="MsoNormal">E.g. Highlight regions of an EM-map in different colours. </div><div class="MsoNormal"><a href="http://www.ebi.ac.uk/pdbe-srv/emsearch/atlas/5134_visualization.html">http://www.ebi.ac.uk/pdbe-srv/emsearch/atlas/5134_visualization.html</a></div><div class="MsoNormal">Regions shouldn’t be mutually exclusive, since current practices don’t ensure this. Combine several masks to produce an image (see link). </div><div class="MsoNormal">Also need this for segmentations. E.g. neurons with parts marked in different colours. </div><div class="MsoNormal"><br></div><div class="MsoNormal"><br></div><div class="MsoNormal">File formats</div><div class="MsoNormal"><br></div><div class="MsoNormal">Good place to look is Chimera code: </div><div class="MsoNormal">Chimera.app/Contents/Resources/share/VolumeData/mrc/</div><div class="MsoNormal"><br></div><div class="MsoNormal">-<span class="Apple-tab-span" style="white-space:pre"> </span>MRC – OK but pixel size not correct</div><div class="MsoNormal">-<span class="Apple-tab-span" style="white-space:pre"> </span>Spider - no pixel size metadata? </div><div class="MsoNormal">-<span class="Apple-tab-span" style="white-space:pre"> </span>Imagic</div><div class="MsoNormal"><br></div><div class="MsoNormal"><br></div><div class="MsoNormal">Ontologies / RDF</div><div class="MsoNormal"><br></div><div class="MsoNormal">Annotate with ontology terms:</div><div class="MsoNormal">-<span class="Apple-tab-span" style="white-space:pre"> </span>Flexible (we don’t have to define metadata structures ahead of time)</div><div class="MsoNormal">-<span class="Apple-tab-span" style="white-space:pre"> </span>Use for searching etc.</div><div class="MsoNormal">-<span class="Apple-tab-span" style="white-space:pre"> </span>Probably won’t use them for reasoning except “is-a” ? </div><div class="MsoNormal">-<span class="Apple-tab-span" style="white-space:pre"> </span>Implement in a similar way to Tagging. </div><div class="MsoNormal"><br></div><div class="MsoNormal"><br></div><div class="MsoNormal">Correlative (Maps and PDB coordinates)</div><div class="MsoNormal"><br></div><div class="MsoNormal">-<span class="Apple-tab-span" style="white-space:pre"> </span>Chimera allows superimposition, docking etc and the state can be saved as a Python script to recreate the session. This script also saves the maps and/or PDB coordinates. But this is not a reliable means of storing these relationships long-term. Not necessarily a stable format etc?</div><div class="MsoNormal">-<span class="Apple-tab-span" style="white-space:pre"> </span>Need some other way to define molecule relationships etc.</div><div><br></div></span></font></div></body></html>