<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi All-<div><br></div><div>Thanks for the follow-up, Guneter.</div><div><br><div><div>On 6 Jun 2010, at 14:16, Guenter Giese wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Guillaume,<br>hi Jason and Andrew,<br><br>this is a major issue for us too.<br><br>My home-built light sheet microscope generates a lot of data, and the microscope configuration as well as the imaging parameters are quite complex, and changed frequently. And a proper storage and retrieval of our metadata is obviously quite important. <br><br>I talked about this with Jason Swedlow and Andrew Patterson at the ELMI Meeting 2009 in Glasgow. They were very interested. Unfortunately, we had not enough time until now to check thoroughly and to decide which parameters are represented by or lacking in the OME schemas. And, since the details of our metadata are not fully settled yet (they may never be!), we did not ask for implementation in the OME schema until now.</blockquote><div><br></div><div>We're happy to do some of the hard work, if you (and Guillaume, and anyone else) just give us a list of what you need, and MOST IMPORTANTLY, example data that you have. That will tell us alot about what you are recording and how you use it.</div><blockquote type="cite"> <br><br>In the meantime, we decided to export the metadata into an XML logfile (trying to foresee possible future implementations in the OME schemas, and actually spend a lot of time on this).<br></blockquote><div><br></div><div>OK, great-- we would certainly be interested in driving this forward with your help.</div><br><blockquote type="cite"><br>Currently a student is working on this (he may be back in the lab in a week). He tries to work around the problem by implementing "Structured Annotations". He is in contact with the OME team too.<br><br>We would also like to discuss this SPIM / OME issue with any other users interested.<br></blockquote><div><br></div><div>As would we. I expect your log file would be a great start-- something we can see and work with. In general, we can't add support for domains we don't know, but if we can get some access to domain expertise, and certainly, great example datasets, that is what we need to do real work.</div><div><br></div><div>Thanks for pushing this and for your help.</div><div><br></div><div>Cheers,</div><div><br></div><div>Jason</div><div><br></div><br><blockquote type="cite"><font class="Apple-style-span" color="#000000"><br></font><br>----- Ursprüngliche Nachricht -----<br>Von: <a href="mailto:gay@cict.fr">gay@cict.fr</a><br>Datum: Freitag, 4. Juni 2010, 18:32<br>Betreff: [Spim-lsfm-info] Ome-tiff and light sheet fluorescence microscopy<br>An: <a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>, <a href="mailto:spim-lsfm-info@lists.sourceforge.net">spim-lsfm-info@lists.sourceforge.net</a><br><br>> Hi lists,<br>> <br>> -- This is posted in parallel to the ome-users an spim mailing <br>> lists --<br>> <br>> Our team in Toulouse is developing a SPIM (Selective Plane <br>> Imaging <br>> Microscope). We whish to use OME TIFF format for our data, as it <br>> seems <br>> the more convenient.<br>> <br>> But the OME-XML schemata lacks some tags that would be useful in <br>> Light <br>> Sheet Microscopy:<br>> - The sample can rotate around an axis, <br>> so we would need a to <br>> specify this angle as a SizeA attribute, as well as change a <br>> little <br>> the DimensionOrder spec, etc.<br>> - We use TWO objectives at a time, one <br>> for illumination and one <br>> for collection, so there should be room for this also.<br>> Plus some other specific stuff I can't see right now.<br>> <br>> So my questions are the following:<br>> What's the best way to do this? Should we add the tags as we <br>> wish, and <br>> create our own shemata and xsd file?<br>> Is there a way to keep our files valid ome-tiff ?<br>> For spim users, has anyone given it a thought already?<br>> <br>> Eventualy, how should we proceed to get those changes somehow <br>> included <br>> in the ome schemata?<br>> <br>> Thank you<br>> <br>> Guillaume Gay, Phd.<br>> <br>> ITAV - Toulouse<br>> <br>> <br>> <br>> <br>> ----------------------------------------------------------------<br>> This message was sent using IMP, the Internet Messaging Program.<br>> <br>> <br>> -----------------------------------------------------------------<br>> -------------<br>> ThinkGeek and WIRED's GeekDad team up for the Ultimate <br>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the <br>> lucky parental unit. See the prize list and enter to win: <br>> <a href="http://p.sf.net/sfu/thinkgeek-promo">http://p.sf.net/sfu/thinkgeek-promo</a><br>> _______________________________________________<br>> Spim-lsfm-info mailing list<br>> <a href="mailto:Spim-lsfm-info@lists.sourceforge.net">Spim-lsfm-info@lists.sourceforge.net</a><br>> <a href="https://lists.sourceforge.net/lists/listinfo/spim-lsfm-info">https://lists.sourceforge.net/lists/listinfo/spim-lsfm-info</a> _______________________________________________<br>ome-users mailing list<br><a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br></blockquote></div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="font-family: Helvetica; "><br class="Apple-interchange-newline"><br class="khtml-block-placeholder"></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">**************************</span></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">Wellcome Trust Centre for Gene Regulation & Expression</font></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">College of Life Sciences</font></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">MSI/WTB/JBC Complex</font></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">University of Dundee</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Dow Street</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Dundee DD1 5EH</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">United Kingdom</span></div><div style="font-family: Helvetica; "><br style="font-family: Helvetica; "></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">phone (01382) 385819</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Intl phone: 44 1382 385819 </span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">FAX (01382) 388072 </span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">email: <a href="mailto:jason@lifesci.dundee.ac.uk">jason@lifesci.dundee.ac.uk</a></span></div><div style="font-family: Helvetica; "><br style="font-family: Helvetica; "></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Lab Page: <a href="http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html">http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html</a></span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Open Microscopy Environment: <a href="http://openmicroscopy.org">http://openmicroscopy.org</a></span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">**************************</span></div><div style="font-family: Helvetica; "><br class="webkit-block-placeholder"></div><div style="font-family: Helvetica; "><div>The University of Dundee is a Scottish Registered Charity, No. SC015096.</div></div><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></div></span> </div><br></div></body></html>