<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Ghislain-<div><br><div><div>On 2 May 2009, at 16:19, Ghislain Bonamy wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>John,<br><br>Unfortunately the flex file format is not up to date in the bioformats, although some of the new metadata is handled. In particular, bioformats is unable to retrieve the number of fields/z-section/channels/time point, which is critical point. </div></blockquote><div><br></div><div>Thanks for this feedback. This is news to us, as we correctly report this metadata from the test files we have. If you have had problems using Bio-Formats, the best thing to do is to send us details, and if possible, the offending files, and we'll certainly work to we fix any problems we find.</div><blockquote type="cite"><div><br>I was hoping to work on this and add this capacity to the format but have not had a chance to it. I have contacted P&K about maybe helping out since they are using Omro a base for their Columbus platform, but I don't think, oddly enough, that they are interested to help. </div></blockquote><div><br></div><div>On the contrary, PerkinElmer (I assume that is who you are referring to) have been very helpful supplying test files. Again, if you have files that might expose something we don't know about, sending us specific details and the data is the best thing to do.</div><div><br></div><blockquote type="cite"><div>Perhaps if enough customer request that they help improving bioformats they might do it. I will try to work on it soon and will keep the Opera users posted. Furthermore, a nice feature would be to be able to keep the metadata from the flex file in addition to the metadata from OME, so that the flex file remains backward compatible with the Epochal (becomes both an ome.tiff and remains a flex file). This feature which could be extended to all TIFF derivative format, may require some serious modifications of bioformats, but I will let the expert (i.e.. Jason) se what they can do about t.<br><br></div></blockquote><div><br></div><div>Can you explain why we should do this? Why doesn't the metadata in OME-TIFF satisfy your needs? Note that we NEVER directly write proprietary formats-- we have enough problems supporting reads of all the variants. Writing as well would be a minefield, and more importantly, breaks the whole concept of supporting interoperability.</div><blockquote type="cite"><div><br><br>On another note bioformats does support the luraware compression, granted hat you provide a license code for it. Logic would suggest that a key would be required to compress with luraware but not to decompress to make the forma at least partially open. This however is not the case. Perhaps P&K should in my opinion provide such license code since the capacity of a user to read an image is obviously a inherent part of their system. However, this may not be part of the agreement they reach with Luraware. In the mean time, saving as uncompressed tiff is the better solution.</div></blockquote><div><br></div><div>We can't comment on PerkinElmer's plans for file formats; we have no knowledge of their plans and agreements and any discussions of this with the community and users is up to them. We do however agree that saving data in uncompressed form often leaves the user with many more options for data handling and analysis.</div><div><br></div><div>Hope that helps. Thanks again for your feedback.</div><div><br></div><div>Cheers,</div><div><br></div><div>Jason</div><div><br></div><br><blockquote type="cite"><div><br><br><br><br>Let me know if you have any other questions.<br><br><br><br>Best,<br><br><br><br> Ghislain Bonamy, PhD <br>_______________________________<br>Genomic Institute of the<br>Novartis Research<br>Foundation<br>Functional Genomics, G214<br>+1 (858) 812-1534 (W & F)<br>+1 (858) 354-7388 (C)<br>www.gnf.org <<a href="http://www.gnf.org/">http://www.gnf.org/</a>> <br><br>HudsonAlpha Instiute for Biotechnology<br><a href="http://www.hudsonalpha.org">www.hudsonalpha.org</a><br><http://www.gnf.org/> <br><br>________________________________<br><br>From: ome-users-bounces@lists.openmicroscopy.org.uk on behalf of John Moffat<br>Sent: Fri 5/1/2009 11:40 PM<br>To: ome-users@lists.openmicroscopy.org.uk<br>Subject: [ome-users] Flex File Format<br><br><br><br>Hi,<br>I was just about to ask the exact same question as the previous <br>poster. Since I'm not using the Lurawave compression (not worth the <br>hassle, in my opinion), is there a way we can activate the <br>PerkinElmer .flex format in the bioformats library?<br><br>Does anyone know if the flex file bioformat is up to date with the <br>newer (Acapella 2) version of the format? Either way, I'd like to test <br>it.<br><br>Thanks<br>John<br><br><br>_______________________________________________<br>ome-users mailing list<br>ome-users@lists.openmicroscopy.org.uk<br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br><br><br>_______________________________________________<br>ome-users mailing list<br>ome-users@lists.openmicroscopy.org.uk<br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br></div></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>