<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Stuart-<div><br></div><div>Thanks for your comments. I may have been the ultimate source, so I'll just clarify what I am pretty sure I said. But this is all a little complicated, and I may not have made myself clear.</div><div><br></div><div>First, as Curtis pointed out. .flex IS supported in Bio-Formats. When we say this, we mean that using Bio-Formats, you can read the .flex format file. However, we don't explicitly guarantee the extent of metadata support. It is almost always at least some of the included metadata, but achieving what we call "metadata completion" (which means we've found a home for every piece of metadata in the file we can identify is a big task. It is one we are working through for a number of files (see the Beta4.0 release announcement on 27 Mar 09), but is certainly a work in progress.</div><div><br></div><div>Second, as you have heard and seen, we are working to support usage of OMERO in HCS. This is a stepwise, progressive effort, where we first deal with the data model (<a href="http://www.ome-xml.org/wiki/ScreenPlateWell)">http://www.ome-xml.org/wiki/ScreenPlateWell)</a>, put this into the OMERO backend (ScreenPlateWell was included in our Beta3 release, released 30 June 08, but we didn't tell anyone), then begin importing data (in the the code for Beta4.0, just not turned on), and then finally deliver full support in all the clients. We want to deliver a working, useful solution for HCS-- that enables real work with the data, and so that takes time. </div><div><br></div><div>So, because of all this, support for files within OMERO is necessarily a subset of files supported in Bio-Formats. As Curtis mentioned, following feedback at our recent OME User's Meeting, we are working on a number of pieces of tech to make it MUCH easier to bring in new file types into OMERO. But, no, full HCS support is not yet available.</div><div><br></div><div>Following the logic above, .flex is supported within Bio-Formats, but we want to ensure that we properly support the various metadata associated with the files. That will still take some time, but if you want to see what's going on, go to the OMERO clients Trac for the current milestone:</div><div><br></div><div><a href="http://trac.openmicroscopy.org.uk/shoola/milestone/OMERO-Beta4.1">http://trac.openmicroscopy.org.uk/shoola/milestone/OMERO-Beta4.1</a></div><div><br></div><div>and search on 'SPW' (that's OME-ese for ScreenPlateWell, or in English, HCS). You'll see we are laying the groundwork for what you are asking about.</div><div><br></div><div>So, you'll want to know when you will have full HCS support. We had planned to release an HCS viewer within OMERO.insight this summer, but our priorities were shifted by the response from the attendees at our User's meeting (we MUST deliver what the community asks for and the meeting is a great way for the community to express its opinions and priorities). The roadmaps show these changed priorities. We are HOPING to release HCS support in Beta-4.1 (targetted 30 Sept 09 release), but we won't be sure we can make that til we get done with the work we are doing now, building infrastructure for moving data in and out of OMERO and also to deal with the data duplication problem. We'll update this list as we get through the next few weeks.</div><div><br></div><div>We're sorry we don't have a full solution for the data you need. We have a limited amount of work we can achieve, and are doing as well as we can with what we have. Note that OME is completely grant-funded. If you want to help drive the development, you can commission Glencoe Software to do work you need, and this work will be contributed to the open source code base. Alternatively, if you have people who can work with our code base on your team, then implementing this facility won't be that hard (if you follow the list, you'll see that a number of people have already done this). If you go through the emails to this list, you'll find comments from people who have found HCS support within OMERO.insight and want to turn it on. You are welcome to do this-- that is the point of open source work-- but it is not supported. </div><div><br></div><div>That's a long answer, and I'd be happy to discuss in more detail-- just contact me directly.</div><div><br></div><div>As always, thanks for your support.</div><div><br></div><div>Cheers,</div><div><br></div><div>Jason</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br><div><div>On 11 Jun 2009, at 22:19, Curtis Rueden wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Stuart,<br><br>Sorry for the confusion. The Bio-Formats library supports the Flex format, so it is only a matter of time before that support is integrated into the OMERO system. For reference, the Bio-Formats web site (<a href="http://www.loci.wisc.edu/ome/formats.html#formats">http://www.loci.wisc.edu/ome/formats.html#formats</a>) lists all supported formats, with blue-highlighted entries also supported by the OMERO server.<br> <br>It is my understanding that an upcoming release of the OMERO.importer client will allow users to toggle which formats are enabled. This would allow you to "turn on" support for Flex within OMERO, with the caveat that any such manually enabled formats have NOT been well tested with the OMERO system, and you may experience quirks or problems.<br> <br>Regarding more thoroughly tested Flex support, I believe it will come at the same time as many of the planned high-content screening improvements to the OMERO system. We recently reprioritized some features due to feedback at this year's OME European Users meeting, and so I am not certain of the timeline for the HCS improvements, but they are definitely still planned.<br> <br>-Curtis<br><br><div class="gmail_quote">On Thu, Jun 11, 2009 at 11:15 AM, Smith, Stuart C <span dir="ltr"><<a href="mailto:Stuart.C.Smith@pfizer.com">Stuart.C.Smith@pfizer.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <div link="blue" vlink="purple" lang="EN-GB"> <div><p>Afternoon, we were hoping to evaluate OME within our organisation to see if it aided our Scientists, but after setting up the server (windows) and installing clients on several peoples PC, we were surprised to find that .flex files were not supported, despite being advised otherwise in the form of a conversation between someone within my organisation and someone associated with OME. Are they any plans to support .flex? or is this a restriction imposed by Perkin Elmer? If so, is there scope for us to implement .flex file support internally within our own organisation? or if we made contributed in some way to the development of OME, would that clear the path for .flex file support within our OME setup?</p><div> <br class="webkit-block-placeholder"></div><p>If you feel this conversation is best carried on outside of this forum, please feel free to email me directly.</p><div> <br class="webkit-block-placeholder"></div><p>Thanks in advance,</p><div> <br class="webkit-block-placeholder"></div><font color="#888888"><p>Stuart</p> </font></div> </div> <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" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br> <br></blockquote></div><br> _______________________________________________<br>ome-devel mailing list<br><a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a><br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel<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: 12px; 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: 0; "><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://www.dundee.ac.uk/lifesciences/swedlow/">http://www.dundee.ac.uk/lifesciences/swedlow/</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><br></div></body></html>