OME and OMERO: Release of OMERO-Beta3

[Jason Swedlow]

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal 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

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