Release of OMERO & Bio-Formats 5.0.0

[Jason Swedlow-2]

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Dear All,

Today we are releasing OMERO and Bio-Formats 5.0.0. This is a full,
production-ready release of OME's new software tools. With this release,
the 4.4.x line enters maintenance mode and while we will continue to
support it throughout 2014, it will only be updated for major bug fixes.
We've provided scripts to upgrade OMERO 4.4.x installations to 5.0.0.

The 5.0.0 release represents a major change in how the OMERO server handles
files at import compared with all previous versions of OMERO. Referred to
as 'OMERO.fs', this change means that OMERO uses Bio-Formats to read your
files directly from the filesystem in their original format, rather than
converting them and duplicating the pixel data for storage. Images saved in
an OMERO 5.0.0 repository can be accessed by other 3rd party software (this
is read-only access).  OMERO also now reports on the file integrity at
upload so you know if your file is safely stored.

Bio-Formats 5.0.0 includes substantially improved  handling of complex
multidimensional datasets, including tile-based formats used in digital
pathology and support for several new file formats; Aperio AFI, Inveon,
MPI-BPC Imspector, Bio-Rad SCN, Yokogawa CellVoyager [1], LaVision
Imspector, PCORAW, and Woolz [2].

In addition, 5.0.0 continues our effort to support new multidimensional
images.  We previously enabled support for FLIM data in OMERO.server, and
the FLIMfit application built by the Imperial team.  We've now added
support for FLIM data in OMERO.insight.

The changes in Bio-Formats and OMERO 5.0.0 are especially important for
sites working with large multi-GB datasets, e.g., long time lapse, HCS and
digital pathology data.  With this foundation, we will deliver support for
other multidimensional modalities (e.g., light sheet microscopy) later in
2014.

Other features of this release are:

For Bio-Formats:
Launched 'bioformats_package.jar', a new bundled plugin for ImageJ to
replace 'loci_tools.jar'
Added support for 8 new formats (see above)
Fixed support for Becker & Hickl .sdt files with multiple blocks
Fixed tiling support for TIFF, Hamamatsu .ndpi, JPEG, and Zeiss .czi files
Added support for populating and parsing ModuloAlong{Z, C, T} annotations
for FLIM/SPIM data
Many bug fixes (especially Nikon ND2, Zeiss .czi, CellWorX)
Updated Bio-Formats tools command line documentation (
http://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/index.html
)
Updated component names, .jar file names, and Maven artefact names
Improved continuous integration testing

The software is available at:
http://downloads.openmicroscopy.org/bio-formats/5.0.0


For OMERO:
Support for password salting to improve server security
Updated indexing to help improve search performance
OMERO.web upgrade to Django 1.6 allowing more flexibility for developing
new web apps
Initial steps towards supporting MATLAB and Jython scripts
CLI plugin allowing access to tags and tag sets from the command line (
http://www.openmicroscopy.org/site/support/omero5/users/command-line-interface.html
)
Modulo (FLIM/SPIM) support in OMERO.insight
Many bug fixes including thumbnails, plates, tables and LDAP
New help guide for installing the plugins needed to use OMERO with ImageJ (
http://help.openmicroscopy.org/imagej.html)
'What's New' summaries for users (
http://www.openmicroscopy.org/site/support/omero5/users/whatsnew.html),
sysadmins (
http://www.openmicroscopy.org/site/support/omero5/sysadmins/whatsnew.html)
and developers (
http://www.openmicroscopy.org/site/support/omero5/developers/whatsnew.html)
to help you quickly identify updates

The software is available at:
http://downloads.openmicroscopy.org/omero/5.0.0

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

In the near future, the OME Consortium will release updates to several
applications, including OMERO.searcher, u-track and several others.

NOTE: Sites that use Java Webstart may see Java security exceptions.
Please see
https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=7410 for more
information.  We are working on obtaining code signing certs and will
deliver signed client builds as soon as we can.

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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