<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Hans-<div><br></div><div>Thanks much. SVI was one of the first commercial entities to adopt and embrace OME-XML, and we very much appreciate your continued support.</div><div><br></div><div>The link for the PDF is on the page:</div><div><br></div><div><a href="http://jcb.rupress.org/content/189/5/777.full.pdf+html">http://jcb.rupress.org/content/189/5/777.full.pdf+html</a></div><div><br></div><div>It's available to me from home, without VPN, so am pretty sure it is publicly available (also, it's now marked 'free access'). You can put that link anywhere, and anyone should be able to download the PDF. Alternatively, send them to the abstract page and they can decide what the want to do (<a href="http://jcb.rupress.org/content/189/5/777.abstract">http://jcb.rupress.org/content/189/5/777.abstract</a>).</div><div><br></div><div>You can link to it, you just can't mirror for the first 6 months. After that, you can mirror, but you just need to attribute the original source.</div><div><br></div><div>Thanks again.</div><div><br></div><div>Cheers,</div><div><br></div><div>Jason</div><div><br></div><div><br><div><div>On 1 Jun 2010, at 17:43, Hans wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear Jason,<br><blockquote type="cite"><br></blockquote><blockquote type="cite">Today, we are publishing a commentary on file formats in the Journal<br></blockquote><blockquote type="cite">of Cell Biology. The full text is available at:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><a href="http://jcb.rupress.org/content/189/5/777">http://jcb.rupress.org/content/189/5/777</a><br></blockquote><br>Excellent initiative! Fabulous!<br>I always hope that someday we can stop wasting our time writing, updating and patching all those crazy formats.<br>Is there a pdf to be found of the paper, somewhere? If I understand correctly, we can start linking to that pdf in 6 months, right?<br><br>Cheers, Hans<br><br><blockquote type="cite"><br></blockquote><blockquote type="cite">The article represents OME's position on the continued explosion of<br></blockquote><blockquote type="cite">file formats in biological imaging. As we move towards more complex<br></blockquote><blockquote type="cite">data, greater opportunities for data sharing and collaboration, and<br></blockquote><blockquote type="cite">rapidly developing image repositories, we strongly contend that the<br></blockquote><blockquote type="cite">current situation must evolve. New file formats should not be created<br></blockquote><blockquote type="cite">with every new software release. At the very least, the option of<br></blockquote><blockquote type="cite">writing data to open, standardized file formats must be supported in<br></blockquote><blockquote type="cite">all software, whether open or proprietary. We understand that<br></blockquote><blockquote type="cite">exceptional cases exists where specialized image data or metadata<br></blockquote><blockquote type="cite">requires proprietary, custom formats. However, our experience with<br></blockquote><blockquote type="cite">OME-XML and Bio-Formats suggests that the great majority of metadata<br></blockquote><blockquote type="cite">can be supported in open data formats. For this reason, we believe<br></blockquote><blockquote type="cite">that the option of writing image data to an open file format that<br></blockquote><blockquote type="cite">includes support for image acquisition metadata should be mandatory in<br></blockquote><blockquote type="cite">all imaging software.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Our article contains a number of recommendations for driving use of<br></blockquote><blockquote type="cite">standardized file formats. Most importantly, we believe that those<br></blockquote><blockquote type="cite">who decide on which platforms to invest in should use their purchasing<br></blockquote><blockquote type="cite">power to demand support for open file formats. Realistically, this is<br></blockquote><blockquote type="cite">the only way these file formats will be universally used and supported.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">In this article, we have announced a new spec, the OME Compliant<br></blockquote><blockquote type="cite">Specification. This simply uses standard OME-XML, and requires that<br></blockquote><blockquote type="cite">all components of the Image Element are filled in. We see this as a<br></blockquote><blockquote type="cite">first step towards a more complete set of metadata for imaging. The<br></blockquote><blockquote type="cite">documentation for the OME Compliant Specification is at:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> <a href="http://ome-xml.org/wiki/CompliantSpecification">http://ome-xml.org/wiki/CompliantSpecification</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">A key point is that an 'OME Compliant' file is as complete as<br></blockquote><blockquote type="cite">possible, but only contains metadata relevant to a specific imaging<br></blockquote><blockquote type="cite">experiment. The expectation is not that every field is filled out<br></blockquote><blockquote type="cite">regardless of the experiment, but that all fields that are relevant to<br></blockquote><blockquote type="cite">an experiment are completed. As an example, PockelCellSetting would<br></blockquote><blockquote type="cite">not be used in most wide-field microscopy experiments, but would be<br></blockquote><blockquote type="cite">mandatory for many multi-photon imaging experiments. The goal of that<br></blockquote><blockquote type="cite">'best-effort' should be to document an experiment as completely as<br></blockquote><blockquote type="cite">possible, so another person could, with the same sample and<br></blockquote><blockquote type="cite">microscope, reproduce the data recorded in the file.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">OME's own file formats, OME-XML and OME-TIFF are well exercised and<br></blockquote><blockquote type="cite">supported by a number of commercial vendors (<a href="http://openmicroscopy.org/site/support/about/partners">http://openmicroscopy.org/site/support/about/partners</a><br></blockquote><blockquote type="cite">). We continue to work to develop and support these formats, and<br></blockquote><blockquote type="cite">welcome any and all feedback on their design, use, and documentation.<br></blockquote><blockquote type="cite">However, we recognize that OME-XML and OME-TIFF do not fulfill all<br></blockquote><blockquote type="cite">requirements for all imaging experiments. Many others (ICS, DICOM,<br></blockquote><blockquote type="cite">NifTI) are available and will be more or less appropriate, depending<br></blockquote><blockquote type="cite">on a specific experiment. Individual scientists should decide which<br></blockquote><blockquote type="cite">of these formats must be supported, and which they will use. The<br></blockquote><blockquote type="cite">critical point is that image data and metadata are complete and openly<br></blockquote><blockquote type="cite">available for viewing and analysis.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">We appreciate any and all feedback on this issue.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">As always, thanks for your support.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Cheers,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Jason<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">**************************<br></blockquote><blockquote type="cite">Wellcome Trust Centre for Gene Regulation& Expression<br></blockquote><blockquote type="cite">College of Life Sciences<br></blockquote><blockquote type="cite">MSI/WTB/JBC Complex<br></blockquote><blockquote type="cite">University of Dundee<br></blockquote><blockquote type="cite">Dow Street<br></blockquote><blockquote type="cite">Dundee DD1 5EH<br></blockquote><blockquote type="cite">United Kingdom<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">phone (01382) 385819<br></blockquote><blockquote type="cite">Intl phone: 44 1382 385819<br></blockquote><blockquote type="cite">FAX (01382) 388072<br></blockquote><blockquote type="cite">email: <a href="mailto:jason@lifesci.dundee.ac.uk">jason@lifesci.dundee.ac.uk</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">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><br></blockquote><blockquote type="cite">Open Microscopy Environment: <a href="http://openmicroscopy.org">http://openmicroscopy.org</a><br></blockquote><blockquote type="cite">**************************<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The University of Dundee is a Scottish Registered Charity, No. SC015096.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-------------- next part --------------<br></blockquote><blockquote type="cite">An HTML attachment was scrubbed...<br></blockquote><blockquote type="cite">URL:<<a href="http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20100531/8f40cdae/attachment-0001.html">http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20100531/8f40cdae/attachment-0001.html</a>><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">------------------------------<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">ome-devel mailing list<br></blockquote><blockquote type="cite"><a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a><br></blockquote><blockquote type="cite"><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">End of ome-devel Digest, Vol 75, Issue 1<br></blockquote><blockquote type="cite">****************************************<br></blockquote><br><br>-- <br>-------------------------------------------------------------------<br>dr. Hans T.M. van der Voort (<a href="mailto:hans@svi.nl">hans@svi.nl</a>)<br>Scientific Volume Imaging b.v., URL: <a href="http://www.svi.nl/">http://www.svi.nl/</a><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></div></blockquote></div><br><div apple-content-edited="true"> <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> </div><br></div></body></html>