OME and OMERO: Release of OMERO3.0-Beta2.2

[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
OMERO3.0-Beta2.2.  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 the OME 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

Screencast videos showing installation and use are at:

http://openmicroscopy.org/howto

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/

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.

PLEASE NOTE:  Upgrading an OMERO.server from Beta-2 to Beta-2.2
requires an update of the database.  See
http://trac.openmicroscopy.org.uk/omero/wiki/OmeroUpgrade for more
info.

**************
What's New in OMERO3-Beta2.2?

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

http://trac.openmicroscopy.org.uk/omero/milestone/3.0-Beta2.2

and

http://trac.openmicroscopy.org.uk/shoola/milestone/3.0-Beta2.2

OMERO.server
-- a series of performance improvements to accelerate image rendering
-- upgrade JBOSS
-- fixed a JBOSS memory leak issue
-- copying rendering settings
-- updates to LDAP support

OMERO.insight
-- substantial updates to the Measurement tool
-- rationalization of multiple windows
-- history of rendering settings
-- support rendering values outside min/max

OMERO.importer
-- UI improvements
-- new file formats (see
http://trac.openmicroscopy.org.uk/omero/wiki/ImporterFormats)
-- fixed bugs in DV and LSM510 formats (thanks to Mike McCaughey at
Vanderbilt for his help with the LSM510 bug!!!!)

Happy imaging!

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 [phone]
Intl phone:  [phone]
FAX   [phone]
email: [hidden email]

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

[Shalin Mehta]

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

Dear All,

 

 Does Omero.importer support zvi and Olympus fluoview TIFF formats well? 

 

Thanks

Shalin

On Nov 11, 2007 7:33 AM, Jason Swedlow <[hidden email]> wrote:

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
OMERO3.0-Beta2.2.  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 the OME 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

Screencast videos showing installation and use are at:

http://openmicroscopy.org/howto

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/

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.

PLEASE NOTE:  Upgrading an OMERO.server from Beta-2 to Beta-2.2
requires an update of the database.  See
http://trac.openmicroscopy.org.uk/omero/wiki/OmeroUpgrade for more
info.

**************
What's New in OMERO3-Beta2.2?

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

http://trac.openmicroscopy.org.uk/omero/milestone/3.0-Beta2.2

and

http://trac.openmicroscopy.org.uk/shoola/milestone/3.0-Beta2.2

OMERO.server
-- a series of performance improvements to accelerate image rendering
-- upgrade JBOSS
-- fixed a JBOSS memory leak issue
-- copying rendering settings
-- updates to LDAP support

OMERO.insight
-- substantial updates to the Measurement tool
-- rationalization of multiple windows
-- history of rendering settings
-- support rendering values outside min/max

OMERO.importer
-- UI improvements
-- new file formats (see
http://trac.openmicroscopy.org.uk/omero/wiki/ImporterFormats)
-- fixed bugs in DV and LSM510 formats (thanks to Mike McCaughey at
Vanderbilt for his help with the LSM510 bug!!!!)

Happy imaging!

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 [phone]
Intl phone:  [phone]
FAX   [phone]
email: [hidden email]

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

--
My co-ordinates:
Shalin Mehta, Graduate student
Graduate Programme in Bioengineering, NUS, Singapore
Mobile: [phone]

[Jason Swedlow]

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

Hi Shalin (et al):

A list of the supported file formats in OMERO is at
http://trac.openmicroscopy.org.uk/omero/wiki/ImporterFormats

OMERO uses the Bio-Formats library
(http://www.loci.wisc.edu/ome/formats.html) for reading proprietary
files.  If you check the list there, you'll see that ZVI and Fluoview
TIFF are listed.  Therefore, these formats are potentially available
within OMERO, however we only 'turn on' a file format in OMERO when we
have a reasonable set of test data and can validate that we are
correctly reading all the available image metadata, preferably from a
few different files that cover 3D, time-lapse, multi-channel, etc.  If
you have  files for a file format that is supported in Bio-Formats but
not turned on in OMERO that you'd be willing to donate for testing
purposes, please let me know off-line.  We'd be happy to provide ftp
access to our test file repository.

Thanks again for your support.

Cheers,

Jason

On Nov 11, 2007 1:31 AM, Shalin Mehta <[hidden email]> wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> Dear All,
>
>  Does Omero.importer support zvi and Olympus fluoview TIFF formats well?
>
> Thanks
> Shalin
>
>
> On Nov 11, 2007 7:33 AM, Jason Swedlow <[hidden email]> wrote:
>
> > 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
> > OMERO3.0-Beta2.2.  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 the OME 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
> >
> > Screencast videos showing installation and use are at:
> >
> > http://openmicroscopy.org/howto
> >
> > 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/
> >
> > 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.
> >
> > PLEASE NOTE:  Upgrading an OMERO.server from Beta-2 to Beta-2.2
> > requires an update of the database.  See
> > http://trac.openmicroscopy.org.uk/omero/wiki/OmeroUpgrade for more
> > info.
> >
> > **************
> > What's New in OMERO3-Beta2.2?
> >
> > Just a very short summary of what's all detailed at:
> >
> > http://trac.openmicroscopy.org.uk/omero/milestone/3.0-Beta2.2
> >
> > and
> >
> > http://trac.openmicroscopy.org.uk/shoola/milestone/3.0-Beta2.2
> >
> > OMERO.server
> > -- a series of performance improvements to accelerate image rendering
> > -- upgrade JBOSS
> > -- fixed a JBOSS memory leak issue
> > -- copying rendering settings
> > -- updates to LDAP support
> >
> > OMERO.insight
> > -- substantial updates to the Measurement tool
> > -- rationalization of multiple windows
> > -- history of rendering settings
> > -- support rendering values outside min/max
> >
> > OMERO.importer
> > -- UI improvements
> > -- new file formats (see
> > http://trac.openmicroscopy.org.uk/omero/wiki/ImporterFormats)
> > -- fixed bugs in DV and LSM510 formats (thanks to Mike McCaughey at
> > Vanderbilt for his help with the LSM510 bug!!!!)
> >
> > Happy imaging!
> >
> > 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 [phone]
> > Intl phone:  [phone]
> > FAX   [phone]
> > email: [hidden email]
> >
> > Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
> > Open Microscopy Environment: http://openmicroscopy.org
> > **************************
> >
>
>
>
> --
> My co-ordinates:
> Shalin Mehta, Graduate student
> Graduate Programme in Bioengineering, NUS, Singapore
>  Mobile: [phone]

--
**************************
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 [phone]
Intl phone:  [phone]
FAX   [phone]
email: [hidden email]

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