Release of OME 5.0.0-rc1

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Melissa Linkert

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Dec 18, 2013, 12:18:32 PM12/18/13
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Dear All,

Today we are making OMERO and Bio-Formats 5.0.0-rc1 available. This is a precursor to a full, production-ready release of 5.0.0 in January. As well as allowing upgrade from 5.0.0-beta1, this release includes an upgrade script for moving from a 4.4.x OMERO server to a 5.0 server. This has been tested on several systems, including a 13 TB production system which we run here in Dundee, and is working well so far. We’ll continue testing and do our best to ensure early adopters will not lose any data. If anyone is in a position to do a test upgrade to 5.0.0-rc1, we would very much value your feedback.

Other features of this release are:

For OMERO:

* Support for password salting to improve server security;
* OMERO.web upgrade to Django 1.6, requiring Python 2.6.5 or later, and allowing more flexibility for developing new web apps;
* Initial steps towards supporting MATLAB and jython scripts;
* Improvements to the OMERO.matlab toolbox;
* CLI plugin allowing access to tags and tag sets from the command line;
* Modulo (FLIM/SPIM) support in OMERO.insight;
* Many bug fixes including thumbnails, plates, tables and ldap

For Bio-Formats:

* Updated Maven build system and launched new Artifactory repository (http://artifacts.openmicroscopy.org);
* Added support for
* Yokogawa CellVoyager [1] (http://www.openmicroscopy.org/site/support/bio-formats5/formats/cellvoyager.html)
* PCORAW (http://www.openmicroscopy.org/site/support/bio-formats5/formats/pcoraw.html)
* Woolz [2] (http://www.openmicroscopy.org/site/support/bio-formats5/formats/woolz.html)
* Bio-Rad SCN (http://www.openmicroscopy.org/site/support/bio-formats5/formats/bio-rad-scn.html)
* LaVision Imspector (http://www.openmicroscopy.org/site/support/bio-formats5/formats/lavision-imspector.html)
* Added support for populating and parsing ModuloAlong{Z, C, T} annotations for FLIM/SPIM data;
* Updated required netCDF and slf4j versions;
* Improvements to Matlab documentation;
* Many bug fixes (especially Nikon ND2, Zeiss CZI, CellWorX)

Also note that Fiji users can now make use of the latest Bio-Formats 5 format support by enabling the Bio-Formats 5 update site (see http://www.openmicroscopy.org/site/support/bio-formats/users/fiji/index.html for more information).

We have also updated our guidance for contributing to OME projects and moved this documentation to its own section (http://www.openmicroscopy.org/site/support/contributing/) to make it easier to find.


The software is available at:

http://downloads.openmicroscopy.org/omero/5.0.0-rc1
http://downloads.openmicroscopy.org/bio-formats/5.0.0-rc1

Upgrade information is at http://www.openmicroscopy.org/site/support/omero5/sysadmins/server-upgrade.html.

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 Jean-Yves Tinevez
[2] Thanks to Bill Hill
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