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ImageJ Analysis
ImageJ analysis is performed using the GDSC plugins for ImageJ. ImageJ and the
plugins must be installed on the OMERO server that runs the scripts. The
following sections describe the install requirements.
ImageJ can be obtained from the ImageJ website:
The scripts have been tested with v1.45+. Newer versions should be supported.
ImageJ can be installed to any location that is visible by the OMERO server.
GDSC ImageJ plugins
ImageJ analysis is performed using the GDSC plugins for ImageJ. These
can be obtained from the GDSC ImageJ plugins website:
The plugins are written to output the results as text which is captured by the
OMERO scripts in a file. The results are then parsed and uploaded to OMERO or
e-mailed to the user.
The GDSC ImageJ plugins should be placed into the 'plugins' folder of the ImageJ
Java Headless mode (Unix only)
ImageJ is run by the scripts using the ImageJ batch mode. This assumes a
headless Java environment (i.e. no graphical output). In this mode ImageJ is
purely an image analysis program with no user interaction. Unfortunately
on the Unix-derived operating system the headless mode still requires a graphics
device when using some of the core libraries. To allow ImageJ to run on an
OMERO server without a configured graphical output various ImageJ classes
have been rewritten to not use the core Java libraries. Only the classes used
by the GDSC plugins have been changed.
The headless.jar with source code is available in the GitHub repository
containing all the GDSC OMERO scripts. Feel free to modify and distribute this
The headless.jar can be installed to any location that is visible by the OMERO
OMERO scripts
The install locations for ImageJ can be configured using variables at the top
of the scripts:
The ImageJ classpath must contain the full path to ij.jar. If using a Unix
operating system the classpath must contain the full path to the headless.jar
before the ij.jar (separated using :).
Default: "/usr/local/ImageJ/headless.jar:/usr/local/ImageJ/ij.jar"
The location of the ImageJ install (v1.45+). The [ImageJ]/plugins directory
must contain the gdsc_.jar ImageJ plugin.
Default: "/usr/local/ImageJ"
The e-mail address that messages are sent from. Make this a valid address so
that the user can reply to the message.
Default: ''
SMTP setup
The OMERO script have the ability to e-mail results to the user. This is done
using the Python modules smtplib and email. The e-mails are sent using the
module defaults, i.e. using a server URL of localhost at port 25. If the host
machine running OMERO has an alternative SMTP configuration then please
consult the system administrator for SMTP set-up details. The OMERO scripts
will have to be updated to use the alternative SMTP server.
Command-line execution
The scripts have been written to allow exceution outside of the OMERO scripting
environment. The scripts will require the OMERO environment is set-up in the
host shell. Details of the required OMERO environment variables can be found
The key is to include the OMERO python libraries on the PYTHONPATH otherwise
the script will not be able to import the OMERO python modules. The ICE_CONFIG
variable can be used to specify the OMERO host. An example configuration for
the C-shell (csh) on a UNIX platform is show below:
setenv OMERO_HOME /usr/local/omero_dist
setenv ICE_HOME /opt/Ice-3.3.1
# Need ICE_HOME python stuff for python scripting API
setenv PYTHONPATH /usr/lib/pymodules/python2.6:${ICE_HOME}/python/:${OMERO_HOME}/lib/python:${PYTHONPATH}
# Used to set the config file for ICE properties.
setenv ICE_CONFIG /home/omero/ice_config
The ice_config file contains the OMERO host:
If the environment is correctly configured the scripts can be called from a
command-line passing the argument 'run':
% ./ run
The script will prompt the user to enter the OMERO connection details (user,
password, server and port). The script then runs using hard-coded parameter
configuration (which can be changed to suit the testing protocol). The command-
line run-mode provides an example of running image analysis using images stored
in OMERO. It also provides a method to debug the scripts before deployment to
the server.
For further details of the GDSC scripts please contact:
Alex Herbert
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