Open Microscopy Environment

Hi all,

I have worked in Emory university (Comprehensive informatics center in medical school) as a student intern.
We are tying to find a tool that enables to support large volume of images because we handle
a quite large volume of images.

first question, What is the maximum size of the image that omero can support ?

second question, I am tying to install omero.server in the cent OS 5.5 and test the functionalities.
finally, I am successful to install omero.server. But, the web system didn't allow me to log in.
It generated error message like 'error: connection not available. please check your user name and password'

also, I am trying to run , 'bin/omero web settings' , to configure web setting. I remembered that I could run this command on 4.1 version of omero server. But, it did not work when I upgraded 4.1 into 4.2 version.
In summary, can I setup 'web setting configuration' again ? If it is, how I can run this command ? (it seems that 4.2 omen do not support this command.. no setting command..)

It would be very helpful if you have any advices or comments.

I attached diagnostics as a reference.

Code: Select all

OMERO Diagnostics Beta4.2.2-r8718-Beta4.2-b56

================================================================================
       
Commands:   java -version                  1.6.0     (/develop/software/java/jdk1.6.0_21/bin/java -- 2 others)
Commands:   python -V                      2.4.3     (/usr/bin/python)
Commands:   icegridnode --version          3.3.1     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.3.1     (/usr/bin/icegridadmin)
Commands:   psql --version                 8.1.22    (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 19322, enabled)
Server:     DropBox                        inactive (disabled)
Server:     FileServer                     active (pid = 19349, enabled)
Server:     Indexer-0                      active (pid = 19352, enabled)
Server:     MonitorServer                  inactive (disabled)
Server:     OMERO.Glacier2                 active (pid = 19354, enabled)
Server:     OMERO.IceStorm                 active (pid = 19355, enabled)
Server:     Processor-0                    active (pid = 19357, enabled)
Server:     Repository-1                   error: node `repo' couldn't be reached:
the node is not active

Server:     Tables-0                       inactive (disabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /home/omerouser/omero/omero_dist/var/log exists

Log files:  Blitz-0.log                    251.0 KB      errors=1    warnings=59 
Log files:  DropBox.log                    2.0 KB        errors=6    warnings=0   
Log files:  FileServer.log                 0.0 KB       
Log files:  Indexer-0.log                  69.0 KB       errors=0    warnings=35 
Log files:  MonitorServer.log              2.0 KB        errors=3    warnings=0   
Log files:  OMEROweb.log                   42.0 KB       errors=23   warnings=0   
Log files:  Processor-0.log                3.0 KB       
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     1.0 KB       
Log files:  master.out                     0.0 KB       
Log files:  Total size                     0.37 MB

Parsing Blitz-0.log:[line:76] => Server restarted <=
Parsing Blitz-0.log:[line:302] => Server restarted <=
Parsing Blitz-0.log:[line:436] => Server restarted <=

Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:PATH=/develop/software/java/jdk1.6.0_21/bin/:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/opt/ibm/db2/V9.7/bin:/usr/lib64/python2.3/site-packages/Ice/
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=(unset)       
Environment:DYLD_LIBRARY_PATH=(unset)     

OMERO data dir: '/OMERO'        Exists? True    Is writable? True
OMERO.web status... DEVELOPMENT: You will have to check status by hand


For X-Y the maximum size we currently support is 4096x4096. We are currently at work on big images. After completion there will be no X-Y image size limit:

http://trac.openmicroscopy.org.uk/ome/m ... RO-Beta4.3

In OMERO Beta 4.2.x there is no bin/omero web settings, OMERO.web is configured using OMERO configuration properties:

http://www.openmicroscopy.org/site/supp ... nstall_web