[ome-users] Status update: OMERO-Beta4.0

[Jason Swedlow]

Dear All-

Happy Monday!

We are just writing to update you on our progress on OMERO-Beta4.0.   
This is a big step for us-- in Beta4, we are making major changes in  
the way the OMERO server and clients work, how they communicate with  
one another, and most importantly, the level of functionality that  
OMERO delivers.  This has been a very ambitious release, based on  
feedback we've had from the community, and most importantly, positions  
us for the functionality we are scheduling over the next year.  Some  
highlights:

--  we have switched our clients completely over to using the ICE  
framework and entirely removed any dependency on JBOSS.  This is a big  
change, removes a substantial amount of overhead, and simplifies our  
communications.

-- we are releasing a brand new client, OMERO.web.  This is our first  
step in developing and releasing a fully functional web browser-based  
client.

-- we have worked very hard on data import, providing a command line  
data import facility, full metadata support for Zeiss LSM510, Zeiss  
ZVI, Leica LEI, API DeltaVision, Metamorph STK files, and substantial  
acceleration of the data import process.

-- we are releasing another new client of OMERO,  called OMERO.fs.  In  
its first release, OMERO.fs is a file notification system-- it can  
monitor specified file systems for arriving image files and initiate  
import for any new files that appear.  Currently, this uses our  
existing import facility-- all data is read into and stored within an  
OMERO server.  More sophisticated functionality, including support for  
multiple repositories and new modes of data import will come in future  
versions.

-- OMERO.insight has been substantially accelerated, includes support  
for much more metadata, an improved projection interface, and now  
fully integrates OMERO.editor.  OMERO.editor has been substantially  
updated as well, to support very unstructured experiments (e.g.,  
protocols from existing .doc files).

-- for the first time, OMERO will support deleting of images.  This is  
a real "it is truly gone" delete.

As you can imagine, we are now testing Beta4 internally and trying to  
identify any bugs.  You can follow our progress at:

http://trac.openmicroscopy.org.uk/omero/milestone/OMERO-Beta4
http://trac.openmicroscopy.org.uk/shoola/milestone/OMERO-Beta4

As we have accelerated and stress-tested OMERO (e.g., working with  
1000's of images at once), we have seen some problems.  Most have been  
fixed, but one of the most insidious is described at:

http://trac.openmicroscopy.org.uk/shoola/ticket/845

Note that this is all due to fundamental problems in Java, which  
affect a number of parts of OMERO.server and OMERO clients.  These  
bugs were first reported months ago and Sun seems to think they are  
low priority.  We, like others, have spent many hours tracking these  
problems, only to track them to Java's underlying libraries.  We are  
examining alternative solutions.  This problem appears as "out of  
memory" errors in OMERO.insight, especially when viewing large numbers  
of images.  We will provide some workarounds in our documentation at  
release.

Our current timeline shows us packaging a Beta4 release candidate next  
Monday (March 2) for testing.  We'll announce this on these lists.

Thanks to all for your patience and feedback-- we really do value your  
comments, and especially any and all constructive criticism.

Cheers,

Jason

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

The University of Dundee is a Scottish Registered Charity, No. SC015096.



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