<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Forwarding to list.<div><br></div><div>Comments from OME devs, and/or from community?</div><div><br></div><div>Cheers,</div><div><br></div><div>Jason<br><div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>From: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Michael Riffle <<a href="mailto:mriffle@u.washington.edu">mriffle@u.washington.edu</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Date: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">10 September 2009 21:41:04 BST</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>To: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><a href="mailto:jason@lifesci.dundee.ac.uk">jason@lifesci.dundee.ac.uk</a></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Subject: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><b>experience with OME</b></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </div><div>Jason,<br><br>My name is Mike Riffle and I work with Trisha Davis over here in Seattle, handling the informatics endeavors for the Yeast Resource Center. As you already know, we've developed a large database of fluorescence microscopy images (YRC Public Image Repository, <a href="http://images.yeastrc.org/)">http://images.yeastrc.org/)</a>, for which I've implemented support for disseminating the data as fully-valid OME TIFF files. Trisha forwarded some email to me (from you) regarding this web site and suggested that I send you some feedback about OME and my experience getting it set up in our site. I know how hard feedback can be to come by, and I'm more than happy to oblige.<br><br>I spent a /lot /of time going over the ample documentation the OME project provides on their websites, and I know that I've barely scratched the surface of all that OME has to offer. My goal was relatively simple: I wanted to distribute the 500,000+ TIFF images and accompanying experimental metadata as OME TIFFs in our public image database. The idea being that users who download these data will be able to plug them directly into software that supports the OME format specifications.<br><br>Accomplishing this task, however, was not entirely trivial. As you know, the XML specification for OME-XML is very extensive. While documentation does exist, I did have some challenges figuring out how our metadata should be mapped onto the elements present in the XML specification. I don't know if the documentation was intended for people doing what I was doing, but expanding the documentation to more generally describe what is meant by each element (from a high-level light microscopy POV) could potentially be beneficial to developers. Also, a high level description or diagram of the data model in terms of items present in most light microscopy experiments, and where these common elements should go in the XML would be great. For example, given 4 emissions/excitation wavelength channels and 6 z-sections of each channel, this is how that data should be organized in an XML file.<br><br>Once I figured out where I thought the metadata should appear in the XML, I set about using the bio-formats Java library to assemble OME TIFFs from my TIFF image data and metadata. I found the bio-formats library to be great and the documentation very helpful. While it's obvious some of the documentation exists as "stubs", it got the job done. I did have some questions about how to do certain things and used the mailing list. Curtis Rueden responded promptly and helped guide me through my problems and I got everything working. I was definitely impressed by his promptness and eagerness to help.<br><br>However, as it turns out, the bio-formats Java library doesn't produce OME-TIFFs that pass validation using the OME-XML validation tool at <a href="http://validator.openmicroscopy.org.uk/">http://validator.openmicroscopy.org.uk/</a>. I talked to Curtis and this is a known problem. I was a bit worried about producing "invalid" OME-TIFFs for distribution in our site, so I went ahead and ended up writing my own code from scratch to produce valid OME-TIFFs. This required me to become even more intimately familiar with the XML specification and all of its particular requirements (such as the fact that it strictly enforces the order of the XML elements in the OME-XML portion of the OME-TIFF file).<br><br>Our site is now producing OME-TIFFs that pass validation at the OME validator and include all of our experimental metadata, so I'm quite pleased. This certainly wouldn't have been possible without all of the great documentation and the help of the OME staff. Overall, it was probably a bit more complicated than it needed to be, but it was a fine experience and I learned a lot about the OME tools and file specification.<br><br>Another suggestion I have is regarding the possibility of adding in support for describing the experiments biologically--particularly relating to describing the tagged proteins, protein tags or dyes used and possibly the ability to include some manual curation from controlled vocabularies, such as the Gene Ontology. I ended up using user-defined elements to include these types of descriptive elements in the OME-TIFF files. I didn't see any official way to include this information, and it definitely seems like information relevant to the data being viewed.<br><br>Again, it was a positive experience and I look forward to learning more about OME and how we can make our data play well with your tools. If you are ever looking for feedback or for anyone to help contribute to the cause, please don't hesitate to ask. I would love to be involved.<br><br>Cheers,<br>Mike<br><br>-- <br>Michael Riffle<br>Research Consultant, Informatics<br>Yeast Resource Center & UW Proteomics Resource<br>University of Washington, Seattle<br><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>