ImageJ and Fiji

Overview

ImageJ is a program to display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images.

Fiji is an enhanced version of ImageJ2 (which itself is an enhancement of ImageJ supporting multi-dimensional data) containing many more 3rd party plugins that extend the functionality of ImageJ.

Version 1.51i of ImageJ and versions 2.0.0, 2.1.2 (based on ImageJ 1.51d, 1.52p) of Fiji are installed on the iCSF.

Restrictions on use

There are no restrictions on accessing ImageJ and Fiji on the iCSF. However users are requested to cite the applications in any publications. Please see the ImageJ citation instructions for further details.

Set up procedure

To access the software you must first load one of the following modulefiles:

# Fiji - enhanced ImageJ
module load apps/binapps/fiji/2.1.2        # Provides ImageJ 1.52p
module load apps/binapps/fiji/2.0.0        # Provides ImageJ 1.51d

# Or original ImageJ
module load apps/binapps/imagej/1.51i

Running the application

Depending which modulefile has been loaded (see above) you can then run the following command at the iCSF command-line:

ImageJ

# or

fiji

If the Fiji modulefile has been loaded you will get a warning message saying:

[WARNING] Your ImageJ installation cannot be updated because it is read-only

This can safely be ignored.

Further info

Updates

None.

Last modified on November 27, 2019 at 4:10 pm by George Leaver