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<div><font size="2">Hi folks,</font></div>
<div><font size="2"> </font></div>
<div><font size="2">Some of you may remember that I have installed OMERO 4.1 on a Linux desktop and a Mac server (and a Mac laptop) here at PNNL. We now would like to try an upgrade on the Mac server to OMERO ver 4.2. </font></div>
<div><font size="2"> </font></div>
<div><font size="2">So - I have taken a look at the upgrade page at</font></div>
<div><font size="2"> </font></div>
<div><font size="2"> <a href="http://openmicroscopy.org/site/support/omero4/server/upgrade"><font color="#0000FF"><u>http://openmicroscopy.org/site/support/omero4/server/upgrade</u></font></a></font></div>
<div><font size="2"> </font></div>
<div><font size="2"> and the process doesn't seem too bad (particularly since it looks like I don't have to update any of the large number of libs OMERO and OMERO.web needs - install of the libs/underlying software was a major task in the initial install, since
all our machines lacked just about everything OMERO needed to run). However, I have seen some emails on the list where people have posted problems as to doing the upgrade to 4.2.</font></div>
<div><font size="2"> </font></div>
<div><font size="2">Is there anything in particular that I should know about doing the upgrade on a Mac server running under OS 10.6? Are any new libs needed (looks like answer is no, but - reassurance would be welcome). </font></div>
<div><font size="2"> </font></div>
<div><font size="2">Ken, Jeremy - have you done the upgrade on your Mac machines at NIH, and do you have any advice to offer?</font></div>
<div><font size="2"> </font></div>
<div><font size="2"> Cheers,</font></div>
<div><font size="2"> Ron</font></div>
<div><font size="2"> </font></div>
<div><font face="Arial, sans-serif" size="2" color="#D47500">___________________________________________</font></div>
<div><font face="Verdana, sans-serif" size="2">Ronald Taylor, Ph.D.</font></div>
<div><font face="Verdana, sans-serif" size="2">Computational Biology & Bioinformatics Group</font></div>
<div><font face="Verdana, sans-serif" size="2">Pacific Northwest National Laboratory</font></div>
<div><font face="Verdana, sans-serif" size="2">902 Battelle Boulevard</font></div>
<div><font face="Verdana, sans-serif" size="2">P.O. Box 999, Mail Stop J4-33</font></div>
<div><font face="Verdana, sans-serif" size="2">Richland, WA 99352 USA</font></div>
<div><font face="Verdana, sans-serif" size="2">Office: 509-372-6568</font></div>
<div><font face="Verdana, sans-serif" size="2">Email: ronald.taylor@pnl.gov</font></div>
<div><font face="Verdana, sans-serif" size="2"> </font></div>
<div><font face="Verdana, sans-serif" size="2"> </font></div>
<div><font size="2">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</font></div>
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<div style="margin-top: 5pt; margin-bottom: 5pt; "><font size="2"> </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Tahoma" size="2"><b>From:</b> ome-users-bounces@lists.openmicroscopy.org.uk [<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk"><font color="#0000FF"><u>mailto:ome-users-bounces@lists.openmicroscopy.org.uk</u></font></a>]
<b>On Behalf Of </b>Jason Swedlow<br>
<b>Sent:</b> Wednesday, July 14, 2010 11:18 AM<br>
<b>To:</b> OME Development; OME-Users OME-Users<br>
<b>Subject:</b> [ome-users] Release of OMERO Beta4.2.0<br>
</font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">Dear All- </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">Today, The OME Consortium (<a href="http://www.openmicroscopy.org/site/about/development-teams"><font color="#0000FF"><u>http://www.openmicroscopy.org/site/about/development-teams</u></font></a>),
is proud to release OMERO-Beta4.2.0. </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">This release is a major step in functionality and stability for OMERO. The full list of features in OMERO, including new features in the OMERO Beta4.2.0, is at </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif"><a href="http://openmicroscopy.org/site/products/feature-list"><font color="#0000FF"><u>http://openmicroscopy.org/site/products/feature-list</u></font></a> </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">Most features are accompanied by a short movie that shows that functionality in action. </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">For full details of the OMERO Beta4.2.0 release, see: </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif"><a href="http://trac.openmicroscopy.org.uk/omero/milestone/OMERO-Beta4.2"><font color="#0000FF"><u>http://trac.openmicroscopy.org.uk/omero/milestone/OMERO-Beta4.2</u></font></a>
</font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">Some highlights: </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">1. Implementation of User & Group Permissions, and data visibility between users. </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">...This is a big change in functionality, adding group level permissions. For existing production systems, please see the pages at </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">* <a href="https://www.openmicroscopy.org/site/support/omero4/server/permissions"><font color="#0000FF"><u>http://www.openmicroscopy.org/site/support/omero4/server/permissions</u></font></a>
</font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">2. Release of more HCS Functionality </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">...updates to the OME SPW Model and improvements in data visualization: </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">* <a href="http://trac.openmicroscopy.org.uk/omero/wiki/WorkPlan/HCSData"><font color="#0000FF"><u>http://trac.openmicroscopy.org.uk/omero/wiki/WorkPlan/HCSData</u></font></a>
</font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">3. SSL connection between OMERO clients and server </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">...for securing passwords used with the improved LDAP plugin:<br>
<br>
* <a href="https://www.openmicroscopy.org/site/support/omero4/server/security"><font color="#0000FF"><u>http://www.openmicroscopy.org/site/support/omero4/server/security</u></font></a><br>
* <a href="https://www.openmicroscopy.org/site/support/omero4/server/install-ldap"><font color="#0000FF"><u>http://www.openmicroscopy.org/site/support/omero4/server/install-ldap</u></font></a> </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">4. Release of full scripting system, accessible from command line and within OMERO.insight, including Figure Export and FLIM Analysis </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">...OMERO.scripts is our image analysis and processing system, that allows you to run essentially any function or analysis within or against OMERO: </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">* <a href="http://www.openmicroscopy.org.uk/site/support/omero4/scripts/"><font color="#0000FF"><u>http://www.openmicroscopy.org.uk/site/support/omero4/scripts/</u></font></a>
</font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">5. ROIs generated in OMERO.insight stored on server; extended use of OMERO.Tables for analysis results </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">6. New file formats and performance improvements for import, through extensions to Bio-Formats, and server-side import histories. </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">...Bio-Formats has been substantially overhauled: </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">* <a href="http://www.loci.wisc.edu/trac/java/milestone/bio-formats-4.2"><font color="#0000FF"><u>http://www.loci.wisc.edu/trac/java/milestone/bio-formats-4.2</u></font></a>
</font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">7. Revamped, fully functional OMERO.web web browser interface for OMERO </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">8. Upgrade of Backend libraries in OMERO.server </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">...we know, it's very technical, and users don't see it, but it is very important and a ton of work, and sets the stage for lots of cool stuff coming soon! </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">...and lots more! </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">The software is available at <a href="http://openmicroscopy.org/"><font color="#0000FF"><u>http://openmicroscopy.org</u></font></a> </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif"><a href="http://openmicroscopy.org/The"><font color="#0000FF"><u>http://openmicroscopy.org/The</u></font></a> full list of features in OMERO, including new features in the
OMERO Beta-4.2, is at <a href="http://openmicroscopy.org/site/products/feature-list"><font color="#0000FF"><u>http://openmicroscopy.org/site/products/feature-list</u></font></a> </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">Most features are accompanied by a short movie that shows that functionality in action. </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">We have a number of other features we will expose (including extensions to the much talked about OMERO.fs) in point releases that follow over the next few months. </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">Our feedback system, OMERO.qa (<a href="http://qa.openmicroscopy.org.uk/"><font color="#0000FF"><u>http://qa.openmicroscopy.org.uk</u></font></a>) is a facility users and
developers can use to log comments and exceptions. OMERO.qa supports uploading of problematic data files, and tracking of responses to any user queries. Moreover, OMERO.qa includes a demo feature: in collaboration with Urban Liebel at Karlsruhe Institute of
Technology, we are providing demo accounts for OMERO. Use the Demo link at qa to contact us if you are interested in this. </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">As always, thanks for your support. </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">Cheers, </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">Jason<br>
</font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">************************** </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; ">Wellcome Trust Centre for Gene Regulation & Expression<font face="Times New Roman, serif"> </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; ">College of Life Sciences<font face="Times New Roman, serif"> </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; ">MSI/WTB/JBC Complex<font face="Times New Roman, serif"> </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">University of Dundee </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">Dow Street </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">Dundee DD1 5EH </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">United Kingdom </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">phone (01382) 385819 </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">Intl phone: 44 1382 385819 </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">FAX (01382) 388072 </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">email: <a href="mailto:jason@lifesci.dundee.ac.uk"><font color="#0000FF"><u>jason@lifesci.dundee.ac.uk</u></font></a> </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">Lab Page: <a href="http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html"><font color="#0000FF"><u>http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html</u></font></a>
</font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">Open Microscopy Environment: <a href="http://openmicroscopy.org"><font color="#0000FF"><u>http://openmicroscopy.org</u></font></a> </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">************************** </font></div>
<div style="margin-top: 5pt; margin-bottom: 5pt; "><font face="Times New Roman, serif">The University of Dundee is a Scottish Registered Charity, No. SC015096.<br>
<br>
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