<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Kees-<div><br><div><div>On 3 Apr 2009, at 17:51, Straatman, Dr K.R. wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><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 lang="EN-GB" link="blue" vlink="purple"><div class="Section1"><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Dear OMERO users,<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">We have been testing OMERO Beta 3.x (the Computer Centre the server side, I the user side) and the improvements I have seen on the website for OMERO 4 are impressive but we had no time to test it yet. </div></div></div></span></blockquote><div><br></div><div>OK-- if you have any problems installing and running, please do contact us. We are on track for a 4.0.1 release later next week, to fix a few bugs. Beta4 is substantial change and functionality upgrade, and a few bugs and simple missed things are to be expected.</div><div><br></div><br><blockquote type="cite"><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 lang="EN-GB" link="blue" vlink="purple"><div class="Section1"><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">We are looking for an imaging storage and backup system and OMERO can do many things I like. However, going through the function descriptions on the website it is not clear for me how to export data from OMERO to for example Imaris software, Huygens deconvolution software or any other analysis package the users might want to use. </div></div></div></span></blockquote><div><br></div><div>This is critical functionality for us-- it's what we refer to the "whole workflow" or "getting in and out". We've worked hard in Beta4 to get as much metadata as possible into OMERO-- our extension of metadata support in a number of file formats and the integration of OMERO.editor into OMERO.insight are examples of this. However, it's time to get data out of OMERO. In Beta4, OMERO.insight creates a report-- a .xls file with thumbnails and annotations. That's a start, and is by no means everything we have to do. We are working hard on an ImageJ plug-in that supports OMERO-Beta4; more details on this will follow in the next week or so. As OME-TIFF is now supported by many commercial imaging applications, we will also work to have OMERO export this format. And finally, for presentation, we are exploring the creation of MPEGs from data stored in OMERO.</div><div><br></div><br><blockquote type="cite"><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 lang="EN-GB" link="blue" vlink="purple"><div class="Section1"><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">I understand from an earlier email from Andrew Patterson, which also has been posted on the list server, that a plugin for ImageJ is being updated and I saw there is also support for MatLab. He also mentioned OMERO.fs. Will this keep the full functionality of OMERO or because the images are on a different location will lose functionality? </div></div></div></span></blockquote><div><br></div><div>I'm not sure what you mean by 'lose functionality'. Initially, OMERO.fs is implemented as a dropbox for files, to enable automatic import. As we move forward, we intend to use OMERO.fs to enable multiple data repositories. Supporting all the different OS's and filesystems is no small feat, but we are trying.</div><div><br></div><br><blockquote type="cite"><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 lang="EN-GB" link="blue" vlink="purple"><div class="Section1"><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">Before I can implement OMERO I have to be sure how to get images out of OMERO, analyse them and put them back into OMERO, if possible without too much fuss.</div></div></div></span></blockquote><div><br></div><div>As you've seen, access via Matlab is currently supported. As an example, we've provided support for Cellprofiler (<a href="http://www.cellprofiler.org">http://www.cellprofiler.org</a>), the data analysis tool released by Anne Carpenter's group at the Broad, via the OMERO Matlab gateway. Bespoke applications, written in C++, Java, and Python can also access data within OMERO. The functionality described above are the next we'll provide. </div><div><br></div><div>Hopefully, that helps. The bad news-- we're not done. The good news-- we are making steps towards everything you want. It is possible that if you start using OMERO now in a limited way, you can follow along with the delivery of new functionality and help us define what you need. </div><div><br></div><div>Cheers,</div><div><br></div><div>Jason</div><br><blockquote type="cite"><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 lang="EN-GB" link="blue" vlink="purple"><div class="Section1"><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; "><o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">Thanks for your help<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">Kees<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 10pt; ">Dr. K.R. Straatman<br>Senior Experimental Officer<br>School of Biological Sciences<br><a href="http://www.le.ac.uk/biochem/microscopy/home.html" style="color: blue; text-decoration: underline; "><span style="color: blue; ">http://www.le.ac.uk/biochem/microscopy/home.html</span></a><br><br>Postal address:<br>Department of Biochemistry<br>Henry Wellcome Building<br>University of Leicester<br>Lancaster Rd.<br>Leicester LE1 9HN<br>UK<br>tel.: + 44 (0)116 229 7085/252 2263<br>fax: + 44 (0)116 229 7031</span><span style="font-size: 10pt; "><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><b><span style="color: red; ">Times Higher Education University of the Year 2008-9<o:p></o:p></span></b></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div></div>_______________________________________________<br>ome-users mailing list<br><a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: blue; text-decoration: underline; ">ome-users@lists.openmicroscopy.org.uk</a><br><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" style="color: blue; text-decoration: underline; ">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br></div></span></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>