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 an installer macro (Installer.ijm). Either unzip the TXT files to the FIJI directory under the subdirectory of  macros/toolsets, or save them to a folder, drag the Installer.ijm file onto FIJI and run it, selecting the location of the macro files when requested.
 - The Macro Toolsets can then be selected by clicking on the >> on the tool bar.

LUT (look up table)

you can also download some useful Look-up tables (FILM LUTs (ZIP)) : Light Blue, Heat Map, Leica Glow, Height and BCGYRM Spectrum. Download the file, unzip and save it to the luts subdirectory of FIJI.

Colour Deconvolution Vectors

you can also download our user-created additional vector sets (Picrosirius red - 2 options, and additional Massons Trichrome for darker samples and a Massons Trichrome for a black background). Download the Colour Deconvolution Vectors (ZIP) text file and save it to the "plugins" subdirectory of FIJI.

Macro Update History

These macros are updated regularly (either use the macro update tool (Calibrate and Batch tools - you have to be a member of FILM and be on the college network or re-download the latest version from the link above).


  • Moved some macros to other toolsets to rationalise them


  • A new Toolset (Prenentation 3) added with 2 new macros. The first, Tilted Rotation Movie, creates a movie, of first a tilt series in the X direction, then secondly rotates this tilted view 360 degrees. the second, 3D Tilt Movie, creates a movie of tilted views from different rotations


  • A new macro added that will produce a 2D image from a line drawn on a time series (X- line length, Y – time). A line is then drawn on this new image along the Y-axis and an intensity profile produced(Extras toolset)


  • Updated the Multi ROI (+15) intensity time plot adding calculate maxima option (Intensity 2 toolset)


  • Added a new macro that numbers the skeleton output from the Analyse Skeleton plugin (Presentation2 toolset) an moved the Invert Z macro to the series toolset.


  • Added a new macro to create frame by frame plot from data macro  (Extras toolset).


  • Added Channel Shift Alignment (pixel based) macro to manually align channels in a multichannel image(Series toolset).


  • Added % cell confluency area macro (ROI_Tools toolset).


  • Added ROI alignment to the multi move ROI tool (ROI_Tools toolset).


  • Added a multi ROI scaling option to the multi move ROI tool (ROI_Tools toolset).


  • A new tool to calculate and display the full width half maximum (FWHM) intensity sum from a line profile (Intesity 2 toolset).


  • A new tool to interactively display the ruler length on the selected image. Options to select arrow or line format as well as colour (ROI_Tools toolset).


  • A new tool to generate a heat map from a results table (Extras toolset)


  • The 3 draw Ferets macros have been replaced by a single updated macro (ROI_Tools toolset)


  • A new tool added that allows all ROI's to be moved by the same amount (ROI_Tools toolset)


  • Orthoview Gallery tool updated - . It now results in a multi panel image of the X-Y profile or projection and X-Z, Y-Z profiles.  Options are available to display the “cut” lines, add a scale bar and to change the separating border width.(Perentation toolset)


  • A new macro tool for creating a height colour coded Z projection with calibration bar. It will work on multi-channel time series images  (Prentation 2  toolsets).
  • Moved the  Add symbols macro to Extras toolset.


  • A new macro tool for creating a Z slice movie attached to the maximum projection of the image stack (Prentation  toolsets).
  • Moved the  Add Graphics to movie tool from Presntation to Presentation 2 toolset and moved Loading mutlichannel z slice image tool from Presenataion 2 to Series toolset


  • A macro tool for adding non-standard text symbols to images (Intensity 2 toolsets).
  • The Cytofluorogram graphic tool for JACop output has been updated (Intensity 2 toolsets).