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OME team,<br>
<br>
Congrats and thanks all on this great milestone.<br>
<br>
One quick question from someone who was somewhat impatient. I had
OMERO 5.1.0-m4 installed on a test server and loaded some data into
that to try out some of the new functionality. Now I updated that to
the released 5.1.0 but it refuses to start up probably due to these
error messages in Blitz-0.log:<br>
<br>
***************************************************************************************<br>
DB version (OMERO5.1DEV__20) does not match omero.properties
(OMERO5.1__1). Please apply a db upgrade.<br>
See
<a class="moz-txt-link-freetext" href="http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/server-upgrade.html">http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/server-upgrade.html</a><br>
***************************************************************************************<br>
<br>
The server-upgrade.html instructions address how to upgrade the DB
from a 5.0.x version but that probably will not work when upgrading
from m4, right? Anything I can do to upgrade or should I just wipe
my DB and create a new one?<br>
<br>
Thanks,<br>
- Damir<br>
<br>
<div class="moz-cite-prefix">On 4/2/2015 5:11 AM, Helen Flynn
(Staff) wrote:<br>
</div>
<blockquote
cite="mid:8E92280E-04C5-4CA4-AC5E-2E40AA6F8845@dundee.ac.uk"
type="cite">
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<div>
<div>Dear All,</div>
<div><br>
</div>
<div>Today we are releasing OMERO and Bio-Formats 5.1.0. This is
a full, production-ready release of OME's new software tools.
With this release, the 5.0.x line enters maintenance mode and
while we will continue to support it throughout 2015, it will
only be updated for major bug fixes and security issues. We
will not be releasing any further updates to the 4.4.x line.</div>
<div><br>
</div>
<div>The 5.1.0 release updates the Data Model to the January
2015 schema (see <a moz-do-not-send="true"
href="http://www.openmicroscopy.org/site/support/ome-model/schemas/january-2015.html">http://www.openmicroscopy.org/site/support/ome-model/schemas/january-2015.html</a>),
including support for units and new more flexible user-added
metadata, improves performance for a number of operations and
formats, especially import times for large datasets such as
HCS and SPIM, fixes many bugs, and features a substantial code
clean-up across the platform and upgrade to OMERO.web.</div>
<div><br>
</div>
<div>Bio-Formats 5.1.0 includes substantially improved
performance with network file systems, and initial version of
a native C++ implementation with its own viewer, improved
support for ImageJ, and support for several new file formats;
CellH5[1], Perkin Elmer Nuance[2], Amnis FlowSight[3], Veeco
AFM, Zeiss .lms, I2I, plus support for writing Vaa3D data[4].</div>
<div><br>
</div>
<div><br>
</div>
<div>Other features of this release are:</div>
<div><br>
</div>
<div><b>For Bio-Formats:</b></div>
<div>
<ul>
<li> Improvements to developer documentation</li>
<li> Improved support for opening and saving ROI data
with ImageJ and other ImageJ improvements/fixes</li>
<li> Updated RandomAccessInputStream and
RandomAccessOutputStream to read and write bits</li>
<li> Bug fixes for many file formats</li>
<li> Fixes and improvements to bfconvert </li>
</ul>
</div>
<div><br>
</div>
<div>Full details can be found at <a moz-do-not-send="true"
href="http://www.openmicroscopy.org/site/support/bio-formats5.1/about/whats-new.html">http://www.openmicroscopy.org/site/support/bio-formats5.1/about/whats-new.html</a></div>
<div><br>
</div>
<div><b>The software is available at:</b></div>
<div><a moz-do-not-send="true"
href="http://downloads.openmicroscopy.org/bio-formats/5.1.0">http://downloads.openmicroscopy.org/bio-formats/5.1.0</a></div>
<div>and the C++ implementation is available from:</div>
<div><a moz-do-not-send="true"
href="http://downloads.openmicroscopy.org/bio-formats-cpp/5.1.0/">http://downloads.openmicroscopy.org/bio-formats-cpp/5.1.0/</a></div>
<div><br>
</div>
<div><b>For OMERO:</b></div>
<div>
<ul>
<li> New key-value pairs annotations for adding
experimental metadata</li>
<li> Improved workflow for rendering settings and parity
between the clients</li>
<li> Import images to OMERO from ImageJ and save ROIs
and overlays from ImageJ to OMERO</li>
<li> Changing groups and delete operations are now
faster</li>
<li> Import times are much improved for large datasets</li>
<li> OMERO.mail lets admins configure the server to
email users </li>
<li> Configurable server download policy for controlling
the download of original files</li>
<li> Many developer updates such as removal of
deprecated methods, updates to OMERO.web and the C++
implementation</li>
</ul>
</div>
<div><br>
</div>
<div>Further details are available on the What's New pages:</div>
<div><a moz-do-not-send="true"
href="http://www.openmicroscopy.org/site/support/omero5.1/users/whatsnew.html">http://www.openmicroscopy.org/site/support/omero5.1/users/whatsnew.html</a>
<a moz-do-not-send="true"
href="http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/whatsnew.html">http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/whatsnew.html</a></div>
<div><a moz-do-not-send="true"
href="http://www.openmicroscopy.org/site/support/omero5.1/developers/whatsnew.html">http://www.openmicroscopy.org/site/support/omero5.1/developers/whatsnew.html</a></div>
<div><br>
</div>
<div>External developers who have not been following the
milestone releases should also read the 5.1.0-m1 to 5.1.0-m5
version histories on
<a moz-do-not-send="true"
href="http://www.openmicroscopy.org/site/support/omero5.1/users/history.html">http://www.openmicroscopy.org/site/support/omero5.1/users/history.html</a></div>
<div><br>
</div>
<div><b>The software is available at:</b></div>
<div><a moz-do-not-send="true"
href="http://downloads.openmicroscopy.org/omero/5.1.0">http://downloads.openmicroscopy.org/omero/5.1.0</a></div>
<div><br>
</div>
<div>Upgrade information is at <a moz-do-not-send="true"
href="http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/server-upgrade.html">http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/server-upgrade.html</a>.</div>
<div><br>
</div>
<div><b>NOTE: PostgreSQL 9.2 is the new minimum required
version. Sysadmins who don't currently meet this will need
to upgrade to a later version, 9.3+ is recommended.</b></div>
<div><b><br>
</b></div>
<div><b>NOTE: Upgrades to OMERO.web break both OMERO.figure
(version 1.0.0 and earlier) and OMERO.webtagging (version
1.1.0 and earlier). We will be releasing updated versions
which are compatible with OMERO 5.1 imminently but in the
meantime, you should not upgrade if you rely on either of
these optional extensions.</b></div>
<div><br>
</div>
<div><br>
</div>
<div>Any problems or comments, please use the OME Forums or
mailing lists:</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://www.openmicroscopy.org/site/community">http://www.openmicroscopy.org/site/community</a></div>
<div><br>
</div>
<div>Regards,</div>
<div><br>
</div>
<div>The OME Team</div>
<div><br>
</div>
<div>[1] Thanks to Christophe Sommer</div>
<div>[2] Thanks to Lee Kamentsky</div>
<div>[3] Thanks to Lee Kamentsky and Sebastien Simard</div>
<div>[4] Thanks to Brian Long</div>
</div>
<div><br>
</div>
<br>
<div>
<div>
<div>Dr Helen Flynn</div>
<div>OME Technical Writer</div>
<div>Centre for Gene Regulation & Expression</div>
<div>Open Microscopy Environment</div>
<div>University of Dundee</div>
<div><a moz-do-not-send="true"
href="http://openmicroscopy.org/">http://openmicroscopy.org</a></div>
</div>
</div>
<br>
<br>
<span style="font-size:10pt;">The University of Dundee is a
registered Scottish Charity, No: SC015096</span>
<br>
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Damir Sudar - Staff Scientist
Lawrence Berkeley Laboratory / Life Sciences Division
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: <a class="moz-txt-link-abbreviated" href="mailto:DSudar@lbl.gov">DSudar@lbl.gov</a>
WWW: <a class="moz-txt-link-freetext" href="http://www.lbl.gov/lifesciences/labs/sudar_lab.html">http://www.lbl.gov/lifesciences/labs/sudar_lab.html</a>
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