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).


  • 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).


  • Two new macro tools added that plot a multichannel line profile from a time series (with and without channel select - Intensity and Intensity 2 toolsets)
  • The Z profile macro has been moved to Intensity 2 toolset


  • A new version of the simple shade correction tool added that uses the same gaussian blur method but then uses a normalisation to the mean intensity for correction (Intensity 2 toolset)
  • The annotated Gallery tool has been updated to allow auto loading of a user-defined image "title" list (Dyes.txt") which is added to the drop down lists. (create the list using Notepad, one dye per line and save it as "Dyes.txt" into the LUT directory of FIJI.


  • A new intensity tool for variable time series data (Intensity 2 toolset). Uses the meta title of each image to store the time( reads/writes/saves/plots and time stamp images)
  • Colour Deconnvolution shortcut tool has been updated with more functionality. This can be used for all colour vector methods   (Calibrate and Batch toolset)


  • 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