[ome-users] OME and OMERO: Release of OMERO3.0-Beta1

Jason Swedlow jason at lifesci.dundee.ac.uk
Fri Feb 2 14:56:34 GMT 2007


The OME project is pleased to announce the release of OMERO3.0- 
Beta1.  OMERO is a Java Enterprise port of the data management and  
visualization functions of the perl-based OME Server.  The OMERO  
Server ships with a JBOSS Application Server, PostgreSQL RDMS, and  
uses three client applications: OMERO.insight, OMERO.importer, and  

All OMERO resources are available at our newly designed software  
download page:


For new initiates, User Guides for OMERO client applications are  
available at our MilestoneDownloads page:


OMERO installation on OS X is all by Mac packages and should be  
automatic.  There are manual install instructions for Linux and OS X  

Please let us know any problems, wishes etc.


Some background and resources:

OMERO3 is a Java EE (formerly J2EE) application designed for the  
JBoss application server.   OMERO3 runs under Linux and OS X and uses  
Hibernate for mapping to a PostgreSQL database (support for MySQL and  
Oracle are in progress, but have been demonstrated; contact us if  
interested).  OMERO3 requires Java1.5.  Our testing has all occurred  
on Pentium IV or AMD 250-series systems, with 1-2 GB RAM and a Gbit  
network connection.  The OMERO3 docs page is at:


Note that this is really for developers.

OMERO.insight is our cross-platform Java client that uses an OMERO3  
server.  OMERO.insight is our first client; OMERO3 is designed to  
support a number of different clients and client platforms (we are  
considering our long-term strategies for client environments).   
OMERO.insight seems to run well under Linux (so far, tested on RHE3),  
Windows XP-SP2, and OS X; the package requires Java1.5.   We have  
used OMERO.insight on laptops with G4, Intel for Mac, and Intel P4  
processors, usually with 0.5 - 1 GB RAM and 100Mbit or Gbit NICs.

OMERO.importer is our data importer.  This is a Java client (requires  
Java1.5), that currently imports data from a client filesystem into  
an OMERO3 server.  For import of external file formats, the OMERO  
project is using BioFormats- see http://loci.wisc.edu/ome/ 
formats.html.  Currently, OMEROImport supports two file formats--  
APLLC DV and MetaMorph's STK.  We are of course working to include  
OMERO.importer as a component of OMERO.insight, as well as supporting  
server-side import.   A major goal is the extension of proprietary  
file format support in OMERO.importer to include all files supported  
in Bio-Formats.  We, along with our colleagues at LOCI, are working  
hard to expand the range of proprietary file formats supported in  
BioFormats.  Stay tuned!

What does OMERO do?  Mostly, image visualization and image data  
management.  There is not yet support for any management of image  
analysis results and data-- this continues to be one of the hallmarks  
of the released OME 2.x server (OME2.6.0 is now available at http:// 
cvs.openmicroscopy.org.uk; we use this system in the lab for large- 
scale image analysis).  The OMERO3-Beta1 package provides the ability  
to organize image data into Projects and Datasets and also user- 
defined CategoryGroups and Categories (see http://openmicroscopy.org/ 
getting-started/manual_classification.html).   In addition, our  
server-based Rendering Engine provides image visualization functions  
in a remote client environment.  Our testing suggests that this that  
is a very useful tool for visualising image data in a client-server  

Note that the OME and OMERO Servers are parallel, complementary  
projects.  They are currently focussing on different function sets--  
see http://www.openmicroscopy.org/software/why2servers.html for more  

We have recognized the importance of getting feedback on the design,  
development, and documentation of OMERO and its clients.  OMERO  
clients include an automatic bug logging system-- using this helps us  
to help you.  As the above web pages suggest, we target our work  
around a series of milestones, and try to produce packages for  
testing these milestones.  These should not be seen as finished,  
released software, but they are tested and (largely) work as  
promised.  They are beta and should demonstrate what OMERO can achieve.

Thanks again for your interest and support.



MSI/WTB Complex
The 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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