[ome-users] OME and OMERO: Release of OMERO-Beta3

[Jason Swedlow]

Hi-

The OME project is pleased to announce the release of OMERO-Beta3.   
OMERO is a Java Enterprise application designed for the management  
and visualization of digital microscopy data.  OMERO includes both  
server and client applications that install on most operating  
systems.  OMERO.server ships with a JBOSS Application Server,  
PostgreSQL RDMS, and uses three client applications: Java-based  
OMERO.insight and OMERO.importer, and a web browser-based  
OMERO.webadmin.  In addition, we are proud to announce our first  
release of OMERO.editor, a standalone tool for experimental protocol  
editing.

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Downloads
All OMERO resources are available at the OME software download page:  
http://openmicroscopy.org/downloads/

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Docs and Help
For new initiates, User Guides for OMERO client applications are  
included with the client packages.  Do have a look and forward any  
questions (see below).  (***NOTE: The User Guides are still for  
Beta2.2, Updates are coming***; please use the screencast videos for  
up-to-date guides on using OMERO clients).

Screencast videos showing installation and use are at http:// 
openmicroscopy.org/howto
(***NOTE:  these movies show the Beta2.2 clients and server.  There  
is new functionality, especially in the clients, in Beta3.  The new  
movies are being prepared now and will be available by July 5.)

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OS X
OMERO.server installation on OS X is by manual package installation  
only.  Supporting OS X 10.4 and 10.5 installation was a bit too  
painful.  There are manual install instructions-- see http:// 
trac.openmicroscopy.org.uk/omero/wiki/OmeroInstall and the screencast  
video at http://www.openmicroscopy.org/howto/.

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Windows
For OMERO.server install on Windows, see http:// 
trac.openmicroscopy.org.uk/omero/wiki/OmeroInstallWindows

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Upgrading the Database
PLEASE NOTE:  Upgrading an OMERO.server  to Beta requires an update  
of the database.  See http://trac.openmicroscopy.org.uk/omero/wiki/ 
OmeroUpgrade for more info.

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OMERO.server Upgrade notification
All OMERO applications now check for available upgrades.  More  
details, see http://trac.openmicroscopy.org.uk/omero/wiki/ 
UpgradeCheck.  (***NOTE: this facility is on by default in  
OMERO.server, but can be turned off; see the doc for more info).

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OMERO.editor
With OMERO-Beta3, we are releasing our first tool for managing  
experimental protocols.  OMERO.editor is a standalone application  
that allows users to define their own experimental protocols and  
record what they did when they did it, and what they used.  
OMERO.editor includes support for external experimental data models  
like PSLID, MAGE, and OME-XML, and also allows access to any ontology  
available through Open Biomedical Ontologies (http:// 
obo.sourceforge.net).

See http://trac.openmicroscopy.org.uk/shoola/wiki/OmeroEditor for  
more info.  There is a link there for a demo movie-- this will appear  
on our Screencast Movies page next week.

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Feedback
Please let us know any problems, wishes etc.  In general, please use  
the ome-users mailing list-- for more info, see

http://openmicroscopy.org/getting-involved/

We have been using these applications in our lab for the last few  
weeks, so hopefully have most of the bugs.  If we've missed anything,  
do let us know.

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Summary

What's New in OMERO3-Beta3?

Just a very short summary of what's all detailed at:

http://trac.openmicroscopy.org.uk/omero/milestone/3.0-Beta3

and

http://trac.openmicroscopy.org.uk/shoola/milestone/3.0-Beta3

OMERO.server
-- release and support of OMERO.Blitz, the flexible interface for  
multi-platform access to OMERO; see http://trac.openmicroscopy.org.uk/ 
omero/wiki/OmeroBlitz
-- many updates to the API
-- Support for StructuredAnnotations; see http:// 
trac.openmicroscopy.org.uk/omero/wiki/StructuredAnnotations
-- An indexing engine to enable text-based search; see http:// 
trac.openmicroscopy.org.uk/omero/wiki/OmeroSearch
-- Access from Matlab and other external applications; see http:// 
trac.openmicroscopy.org.uk/omero/wiki/OMEROJava
-- for a full description, see http://trac.openmicroscopy.org.uk/ 
omero/wiki/ServerDesign

OMERO.insight
-- Fully integrated tagging system
-- Redesigned user interface
-- Improved thumbnail loading
-- Support for StructuredAnnotations (you can now attach any  
structured data to your OMERO data)
-- Note that previous tags in Beta2.3 have been changed to Projects  
and Datasets; for instructions on how to fix this, see http:// 
trac.openmicroscopy.org.uk/omero/wiki/ProdatasetTotags

OMERO.importer
-- More fully developed Import History
-- Support for OME-TIFF and OME-XML
-- Many new file formats (see http://trac.openmicroscopy.org.uk/omero/ 
wiki/ImporterFormats)

OMERO.editor
-- First Release!!!!!
-- support for user defined protocols, external data models and  
ontologies
-- experiments recorded with a calendar, exported with .ics files

Happy imaging (and have a great summer!)

Cheers,

Jason

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Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone (01382) 385819
Intl phone:  44 1382 385819
FAX   (01382) 388072
email: jason at lifesci.dundee.ac.uk

Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
Open Microscopy Environment: http://openmicroscopy.org
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