[ome-users] OME and OMERO: Release of OMERO3.0-Beta2

[Jason Swedlow]

Hi-

The OME project is pleased to announce the release of OMERO3.0- 
Beta2.  OMERO3 is a Java Enterprise application designed for the  
management and visualization of digital microscopy data.  OMERO3  
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.

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

http://openmicroscopy.org/downloads/

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

http://trac.openmicroscopy.org.uk/omero/wiki/MilestoneDownloads

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

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/

**************
What's New in OMERO3-Beta2?

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

http://trac.openmicroscopy.org.uk/omero/milestone/3.0-Beta2

and

http://trac.openmicroscopy.org.uk/shoola/milestone/3.0-Beta2

OMERO.server
-- a series of performance improvements to accelerate image rendering
-- fix too many file handles issue
-- addition of WebAdmin tool, a browser-based server administration  
tool.
-- new Blitz server that supports access from C/C++ clients  
applications.

OMERO.insight
-- Enhancements to image viewer
-- View and access user data within groups
-- Improved image output
-- Improved display of annotations

OMERO.importer
-- new file formats; currently supporting: DeltaVision (.dv), LSM510  
(.lsm), Metamorph (.stk, with support for.nd), Bio-Rad (.pic), TIFF  
(.tif)
-- UI enhancements (update file system, easier workflow)

OMERO.admin
-- This tool, first released in Beta1, has been removed, in favor of  
a new web-based server admin tool, WebAdmin included with  
OMERO.server.  Do not use OMERO.admin from OMERO3-Beta1 with a Beta2  
server.

Note that we will be releasing more demo videos, like the one at  
http://openmicroscopy.org/howto/.  It just takes some time....  ;-)!


*************

Some background and resources:

OMERO.server is a Java EE (formerly J2EE) application designed for  
the JBoss application server.   OMERO.server 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).  OMERO.server requires Java1.5 but has  
been successfully run on Linux under Java1.6.  Our testing has all  
occurred on Pentium IV or AMD 250-series systems, with 1-2 GB RAM and  
a Gbit network connection.

The OMERO docs page is at:

http://trac.openmicroscopy.org.uk/omero

Note that this is really for developers, but includes information for  
installation, configuration, etc.

OMERO.insight is our cross-platform Java client that accesses an  
installed OMERO server.  OMERO.insight is our first client;  
OMERO.server 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 OMERO server.  For import of external file formats, the OMERO  
project is using BioFormats- see http://loci.wisc.edu/ome/ 
formats.html.  Currently, OMERO.importer supports six file formats--  
APLLC DV, MetaMorph's STK (with .nd), Zeiss LSM510, Leica Confocal,  
Bio-Rad confocal and straight TIFF.  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-Beta2 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  
environment.

Note that we will release OMERO3-Beta2.1 in the next few weeks  
(http://trac.openmicroscopy.org.uk/shoola/milestone/3.0-Beta2.1).   
This will include our first client side measurements of ROIs and is  
the beginning of our work on supporting a variety of image analysis  
functions in OMERO.

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.  In addition, you can file comments with us using the  
Help pulldown-- we appreciate all feedback and always ask that you  
provide as much detail as possible (even, if necessary, examples of  
real data).   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.

Cheers,

Jason


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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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