Example of FIJI image analysis

FIJI (FIJI is just ImageJ)

  • Free open source image processing package
  • Opens all our native file formats
  • Compatible with Windows, Mac and Linux
  • FIJI is a version of ImageJ that will automatically update and load a variety of useful plugins including the Bio-Formats Importer
  • View and edit original image file formats 
  • Measurements and analysis tools
  • Image presentation
  • Wide selection of plugins
  • Macros and macro writing

FILM staff can provide FIJI training and help with macro writing


Download FIJI (FIJI Is Just ImageJ)

Using FIJI

Quick Start Guide to Using FIJI (PDF)


We have a written a few macros to help with presentation and analysis which you can download
(download and save the text file to the macros\toolsets directory of FIJI. It can then be loaded by selecting it using the >> on the FIJI toolbar)

Macro Description (PDF)



Download the file Macros (ZIP)  containing all the macros and unzip it to the FIJI directory under the subdirectory of  macros/toolsets.

The Macro Toolsets can then be selected by clicking on the >> on the tool bar.

LUT (look up table)

you can also download the "Light Blue LUT" LUT, unzip and save it to  the luts subdirectory of FIJI


Macro Update History

These macros are updated regularly (either use the macro update tool or download latedset version).


  • Image information Tool - creates a graphic summary of the image dataset  (Calibrate and Batch toolset) added


  • Tool for overlaying and combining 2 RGB colour images  (Calibrate and Batch toolset) added


  • A multi 3D projection tool added (presentation) - Creates a series of rotations from the 3D projection command which are then concatenated into one series. Options for each rotation step (type, axis, direction, start, range, step, etc).
  • Simple shade correction tool moved to Intensity 2 toolset


  • Ratio time plot tools (single and multi ROI) - combined Intensity  and ratio plots with channel select  (Intensity 2 toolset) added


  • New multiimage Gallery tool  (Presentation toolset) added
  • Library image split and save tool (.lif and .czi files) (Series toolset) added