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Description and Overview

ImageJ is a public domain Java image processing program inspired by NIH Image. Fiji means Fiji is Just ImageJ, and stands for a customization of ImageJ with tools to handle microscope data.

ImageJ/Fiji can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations. 

ImageJ was designed with an open architecture that provides extensibility via Java plugins. Custom acquisition, analysis and processing plugins can be developed using ImageJ's built in editor and Java compiler. User-written plugins make it possible to solve almost any image processing or analysis problem.

Fiji is an integrated suite of software facilities for image enhancement, feature extraction, pattern matching and graphical display. It includes

  • a variety of image readers for easy handling and storage of data,
  • a suite of operators for calculations on multidimensional arrays,
  • a large, coherent, integrated collection of  tools for geometric transformations such as scaling, rotation and flips,
  • graphical facilities for image analysis, movie generation and display either on-screen or on hardcopy, and
  • a well-developed, simple and effective API for Java programming, including a built-in editor and Java compiler.


Type the following command to launch Fiji:

$module load fiji 

Using Fiji on NERSC Systems

 You can running Fiji interactively both on Carver, Hopper and Edison. After logging into one of these machines, you and issue the following:

%qsub -I -V -q interactive -l mppwidth=48
%module load fiji
%fiji &

The Vis/Analytics group has optimized compute nodes to deal with large data files, as those produced by experimental scientists. Particularly on Carver, you can issue:

%qsub -I -V -q interactive -l nodes=4:ppn=2 -l pvmem=15GB -l walltime=00:30:00 
%module load fiji --mem=15360m
%fiji &

Instead of running Fiji interactively, you can run your macro/java code in headless mode. Below, see how to run a macro headless:

%fiji --mem=1000m --headless -macro 'your_macroCode_name' -batch


Extensive on-line documented sample code is available. 


This is one of the essential ImageJ/Fiji tutorials.


PackagePlatformCategoryVersionModuleInstall DateDate Made Default
Fiji carver applications/ visualization 1.47h fiji/1.47h 2013-03-18
Fiji edison applications/ visualization 1.47 fiji/1.47 2014-05-30
Fiji edison applications/ programming CD fiji/CD 2015-02-17 2015-02-17
Fiji hopper_cle52 applications/ programming CD fiji/CD 2015-02-18 2015-02-18