[ome-users] Question regarding upgrade to OMERO 4.2 on a Mac server

Taylor, Ronald C ronald.taylor at pnl.gov
Thu Aug 5 20:24:01 BST 2010

Hi folks,

Some of you may remember that I have installed OMERO 4.1 on a Linux desktop and a Mac server (and a Mac laptop) here at PNNL. We now would like to try an upgrade on the Mac server to OMERO ver 4.2.

So - I have taken a look at the upgrade page at


 and the process doesn't seem too bad (particularly since it looks like I don't have to update any of the large number of libs OMERO and OMERO.web needs - install of the libs/underlying software was a major task in the initial install, since all our machines lacked just about everything OMERO needed to run). However, I have seen some emails on the list where people have posted problems as to doing the upgrade to 4.2.

Is there anything in particular that I should know about doing the upgrade on a Mac server running under OS 10.6? Are any new libs needed (looks like answer is no, but - reassurance would be welcome).

Ken, Jeremy - have you done the upgrade on your Mac machines at NIH, and do you have any advice to offer?


Ronald Taylor, Ph.D.
Computational Biology & Bioinformatics Group
Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, Mail Stop J4-33
Richland, WA  99352 USA
Office:  509-372-6568
Email: ronald.taylor at pnl.gov


From: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Jason Swedlow
Sent: Wednesday, July 14, 2010 11:18 AM
To: OME Development; OME-Users OME-Users
Subject: [ome-users] Release of OMERO Beta4.2.0

Dear All-
Today, The OME Consortium (http://www.openmicroscopy.org/site/about/development-teams), is proud to release OMERO-Beta4.2.0.
This release is a major step in functionality and stability for OMERO. The full list of features in OMERO, including new features in the OMERO Beta4.2.0, is at
Most features are accompanied by a short movie that shows that functionality in action.
For full details of the OMERO Beta4.2.0 release, see:
Some highlights:
1. Implementation of User & Group Permissions, and data visibility between users.
...This is a big change in functionality, adding group level permissions. For existing production systems, please see the pages at
* http://www.openmicroscopy.org/site/support/omero4/server/permissions<https://www.openmicroscopy.org/site/support/omero4/server/permissions>
2. Release of more HCS Functionality
...updates to the OME SPW Model and improvements in data visualization:
* http://trac.openmicroscopy.org.uk/omero/wiki/WorkPlan/HCSData
3. SSL connection between OMERO clients and server
...for securing passwords used with the improved LDAP plugin:

* http://www.openmicroscopy.org/site/support/omero4/server/security<https://www.openmicroscopy.org/site/support/omero4/server/security>
* http://www.openmicroscopy.org/site/support/omero4/server/install-ldap<https://www.openmicroscopy.org/site/support/omero4/server/install-ldap>
4. Release of full scripting system, accessible from command line and within OMERO.insight, including Figure Export and FLIM Analysis
...OMERO.scripts is our image analysis and processing system, that allows you to run essentially any function or analysis within or against OMERO:
* http://www.openmicroscopy.org.uk/site/support/omero4/scripts/
5. ROIs generated in OMERO.insight stored on server; extended use of OMERO.Tables for analysis results
6. New file formats and performance improvements for import, through extensions to Bio-Formats, and server-side import histories.
...Bio-Formats has been substantially overhauled:
* http://www.loci.wisc.edu/trac/java/milestone/bio-formats-4.2
7. Revamped, fully functional OMERO.web web browser interface for OMERO
8. Upgrade of Backend libraries in OMERO.server
...we know, it's very technical, and users don't see it, but it is very important and a ton of work, and sets the stage for lots of cool stuff coming soon!
...and lots more!
The software is available at http://openmicroscopy.org<http://openmicroscopy.org/>
http://openmicroscopy.org/The full list of features in OMERO, including new features in the OMERO Beta-4.2, is at http://openmicroscopy.org/site/products/feature-list
Most features are accompanied by a short movie that shows that functionality in action.
We have a number of other features we will expose (including extensions to the much talked about OMERO.fs) in point releases that follow over the next few months.
Our feedback system, OMERO.qa (http://qa.openmicroscopy.org.uk<http://qa.openmicroscopy.org.uk/>) is a facility users and developers can use to log comments and exceptions. OMERO.qa supports uploading of problematic data files, and tracking of responses to any user queries. Moreover, OMERO.qa includes a demo feature: in collaboration with Urban Liebel at Karlsruhe Institute of Technology, we are providing demo accounts for OMERO. Use the Demo link at qa to contact us if you are interested in this.
As always, thanks for your support.

Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
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<mailto:jason at lifesci.dundee.ac.uk>
Lab Page: http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html
Open Microscopy Environment: http://openmicroscopy.org
The University of Dundee is a Scottish Registered Charity, No. SC015096.

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