[ome-devel] Release of OMERO & Bio-Formats 5.1.0

Thu Apr 2 20:36:47 BST 2015

OME team,

Congrats and thanks all on this great milestone.

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:

***************************************************************************************
DB version (OMERO5.1DEV__20) does not match omero.properties 
(OMERO5.1__1). Please apply a db upgrade.
See 
http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/server-upgrade.html
***************************************************************************************

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?

Thanks,
- Damir

On 4/2/2015 5:11 AM, Helen Flynn (Staff) wrote:
> Dear All,
>
> 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.
>
> The 5.1.0 release updates the Data Model to the January 2015 schema 
> (see 
> http://www.openmicroscopy.org/site/support/ome-model/schemas/january-2015.html), 
> 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.
>
> 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].
>
>
> Other features of this release are:
>
> *For Bio-Formats:*
>
>   *     Improvements to developer documentation
>   *     Improved support for opening and saving ROI data with ImageJ
>     and other ImageJ improvements/fixes
>   *     Updated RandomAccessInputStream and RandomAccessOutputStream
>     to read and write bits
>   *     Bug fixes for many file formats
>   *     Fixes and improvements to bfconvert
>
>
> Full details can be found at 
> http://www.openmicroscopy.org/site/support/bio-formats5.1/about/whats-new.html
>
> *The software is available at:*
> http://downloads.openmicroscopy.org/bio-formats/5.1.0
> and the C++ implementation is available from:
> http://downloads.openmicroscopy.org/bio-formats-cpp/5.1.0/
>
> *For OMERO:*
>
>   *      New key-value pairs annotations for adding experimental metadata
>   *      Improved workflow for rendering settings and parity between
>     the clients
>   *      Import images to OMERO from ImageJ and save ROIs and overlays
>     from ImageJ to OMERO
>   *      Changing groups and delete operations are now faster
>   *      Import times are much improved for large datasets
>   *      OMERO.mail lets admins configure the server to email users
>   *      Configurable server download policy for controlling the
>     download of original files
>   *      Many developer updates such as removal of deprecated methods,
>     updates to OMERO.web and the C++ implementation
>
>
> Further details are available on the What's New pages:
> http://www.openmicroscopy.org/site/support/omero5.1/users/whatsnew.html http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/whatsnew.html
> http://www.openmicroscopy.org/site/support/omero5.1/developers/whatsnew.html
>
> 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 
> http://www.openmicroscopy.org/site/support/omero5.1/users/history.html
>
> *The software is available at:*
> http://downloads.openmicroscopy.org/omero/5.1.0
>
> Upgrade information is at 
> http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/server-upgrade.html.
>
> *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.*
> *
> *
> *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.*
>
>
> Any problems or comments, please use the OME Forums or mailing lists:
>
> http://www.openmicroscopy.org/site/community
>
> Regards,
>
> The OME Team
>
> [1] Thanks to Christophe Sommer
> [2] Thanks to Lee Kamentsky
> [3] Thanks to Lee Kamentsky and Sebastien Simard
> [4] Thanks to Brian Long
>
>
> Dr Helen Flynn
> OME Technical Writer
> Centre for Gene Regulation & Expression
> Open Microscopy Environment
> University of Dundee
> http://openmicroscopy.org <http://openmicroscopy.org/>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
>
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel

-- 
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: DSudar at lbl.gov
WWW: http://www.lbl.gov/lifesciences/labs/sudar_lab.html

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