Warning

Iceberg reaches end-of-life on 30th November 2020. If you are running jobs on Iceberg then you need to take urgent action to ensure that your jobs/scripts will run on ShARC or Bessemer. If you have never used ShARC or Bessemer then now is the time to test your scripts. Not all software on Iceberg is available on ShARC/Bessemer.

ImageJ¶

ImageJ is a public domain, Java-based image processing program developed at the National Institutes of Health.

Interactive Usage¶

After connecting to Iceberg (see Establishing a SSH connection), start an interactive session with the qrshx command.

The latest version of ImageJ (currently 1.50g) is made available with the command

module load apps/binapps/imagej

Alternatively, you can load a specific version with

module load apps/binapps/imagej/1.50g

This module command also changes the environment to use Java 1.8 and Java 3D 1.5.2 An environment variable called IMAGEJ_DIR is created by the module command that contains the path to the requested version of ImageJ.

You can start ImageJ, with default settings, with the command

imagej

This starts imagej with 512Mb of Java heap space. To request more, you need to run the Java .jar file directly and use the -Xmx Java flag. For example, to request 1 Gigabyte

java -Xmx1G -Dplugins.dir=$IMAGEJ_DIR/plugins/ -jar $IMAGEJ_DIR/ij.jar

Documentation¶

Links to documentation can be found at http://imagej.nih.gov/ij/download.html

Installation notes¶

Install version 1.49 using the install_imagej.sh script

Run the GUI and update to the latest version by clicking on Help > Update ImageJ

Rename the run script to imagej since run is too generic.

Modify the imagej script so that it reads:

java -Xmx512m -jar -Dplugins.dir=/usr/local/packages6/apps/binapps/imagej/1.50g/plugins/ /usr/local/packages6/apps/binapps/imagej/1.50g/ij.jar

ImageJ’s 3D plugin requires Java 3D which needs to be included in the JRE used by imagej. I attempted a module-controlled version of Java3D but the plugin refused to recognise it. See https://github.com/rcgsheffield/sheffield_hpc/issues/279 for details.

The plug-in will install Java3D within the JRE for you if you launch it and click Plugins>3D>3D Viewer

Modulefile¶

The module file is on the system at /usr/local/modulefiles/apps/binapps/imagej/1.50g

Its contents are:

#%Module1.0#####################################################################
##
## ImageJ 1.50g modulefile
##

## Module file logging
source /usr/local/etc/module_logging.tcl
##

module load apps/java/1.8u71

proc ModulesHelp { } {
      puts stderr "Makes ImageJ 1.50g available"
}


set version 1.50g
set IMAGEJ_DIR /usr/local/packages6/apps/binapps/imagej/$version

module-whatis   "Makes ImageJ 1.50g available"

prepend-path PATH $IMAGEJ_DIR
prepend-path CLASSPATH $IMAGEJ_DIR/
prepend-path IMAGEJ_DIR $IMAGEJ_DIR