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 the "Light Blue LUT" LUT, 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).


  • The Picro-Sirius Red analysis tool has been replaced with a general Colour Deconnvolution shortcut tool. This can be used for all colour vector methods   (Calibrate and Batch toolset)


  • A new tool to interactively measure a line on an image (ROI_tools and Extras toolsets).


  • A new tool to generate a grid or ROI's (ROI_tools toolset).
  • A new tool to split a Picro-Sirius Red image into its component parts (Calibrate and Batch toolset)
  • Some tools have been moved to other toolsets .
  • New Extras toolset added.


  • A new tool to generate cells in random positions in a Z stack and if the image is a time series then also generate random movement of these cells over time. Options to use the format from an open existing image or to create a new image, control of number and size of cells and the maximum distance allowed for their movement. Additional options to create or use exclusion/inclusion ROI’s.


  • A new tool to create a combined zooming and panning movie from a single image. Options to format images and add scale bar  (Presentation toolset).
  • The White balance tool has been moved to the Calibrate and Batch toolset


  • A new tool to create a crop panning movie from a single image. Options to format images and add scale bar  (Presentation toolset).


  • A new tool to calibrate the re-sampled images from the Bio-Formats importer for tiles where only the full format is calibrated


  • A new tool to add a single channel fixed image to a time series (Presentation 2 toolset).


  • Lambda intensity tool updated to multi ROI and image projection. New tools to generate LUT's from wavelenth and also from RGB selection (Presentation 2 toolset).


  • General update and reorganisation.


  • A new tool to create a zoom movie from a single image. Options to add scale bar and mask frame and also the number of images (Presentation toolset).


  • A new tool to create an intensity plot that can be joined to an image series displaying intensity changes frame by frame for a single channels (limited to 10 ROI’s) (Intensity Toolset)


  • An updated version of the ROI time plot tool to allow more than 15 ROI's to be selected (Intensity 2 Toolset) .


  • A new tool to reverse the order of the Z slices in a multichannel hyperstack - also works on a time-Z series (Presentation 2 Toolset) .


  • A new tool for creating a colour height map from a Z-stack using threshold. Included are options to add a calibration bar and re-size image (Presentation 2 Toolset) .


  • A new tool for creating a colour thickness map from a Z-stack using threshold. Included are options to add a calibration bar and re-size image (Presentation 2 Toolset) .


  • A new tool for measureing the area of a Scratch/wound assay image (ROI_Tools Toolset)


  • A new tool for inserting a "Inset" Z-Stack into a larger Z-stack eg for changing the output of the 3D Gallery tool (Presentation 2 Toolset) 


  • A new tool for creating a fancy cytofluorogram using the data produced from the JACoP Co-Localisation plugin (Presentation 2 Toolset).
  • A new tool for creating a colour orientation scale for use with images generated using the Orientation J Plugin (Presentation 2 Toolset).


  • A new tool to Join together multichannel Z stacks, set LUT's and reset brightness and contrat to Min Max. Useful for loading the de-convolved images from Huygens (Presentation 2 Toolset).


  • New toolset "Presentation 2" added to include Image information Tool - creates a graphic summary of the image dataset  (Calibrate and Batch toolset) added and aslo an auto brightness and contrast reset tool. Presentation crop tool updated to correct for errors.


  • 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