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Where to find general ImageJ Information:

Main ImageJ website

ImageJ Documentation

click on “ImageJ User Guide” (not the PDF)

See sidebar on left for all of the menu commands and their descriptions.

For overview of basic image manipulation: 25 Image

includes Brighness/Contrast, Thresholding, Color thresholding, Splitting/Merging channels, Stacks, ie maxProjections, reslicing, 3D volume etc

For overview of basic image processing: 26 Process

This is a great introduction to basic image processing methods available in ImageJ and how they work. It's a great starting point. The next step is then to go to the plugins page and look around what other tools are already available (

For overview of the ImageJ Editor to run macros, scripts, and plugins: 21 ImageJ Editor

ImageJ Macro information:

On main ImageJ Documentation website, click on “resources”

Introduction to Macro Language: Includes the syntax for inf/else statements etc and other general useful information. Worth reading through!

Built-in Macro functions

This is one of the most important pages. It lists all of the functions available to write macros. If you have the time, it is worth reading/skimming through all of them to know what is possible.

Introduction into Macro Programming (via FIJI) This is Fiji's Macro intro. It is also relevant for those of you running ImageJ proper.

Example Macros

ImageJ vs. FIJI

Fiji website:

  • “Fiji is just imageJ” except that the macro-editor is different
  • if open a macro written in ImageJ or text editor in FIJI, need to tell FIJI what language it is
  • FIJI also has MIJI capability: combine ImageJ and Matlab!

Useful shortcuts/tips

  • always duplicate your file before playing with it. Will allow you to keep the original file open and repeat if you make a mistake. And will ensure you don't accidentally alter the original data
  • command-shift-T for threshold window
  • command-shift-C for the brightness/contrast window
  • command-shift-D for duplicate
  • command-shift-E for “remake previously selected shape”
  • T to add a shape to the ROI manager
  • command-R inside macro editor to run a macro or a selected line in the macro
  • up and down arrows to mag up or down
  • left/right arrows to scroll through a one-color z-stack

6. Other macro functions of use that came up during class, all described on the MacroFunction list webpage:

  • getFileList(path)
  • listname.length
  • listname[i]
  • substring(string,start,stop)
  • indexOf(name, firstInstanceOf)
  • roiManager(cmd)
  • runMacro(name)
  • setAutoThreshold(method) and getThreshold(lower, upper)
  • setResult(“Column”, row, value)
  • SetPixel(x,y,value)
  • …and many more
/var/www/html/dokuwiki/data/pages/imagej_introduction.txt · Last modified: 2011/08/24 11:40 (external edit)