How to install and use Jython with ImageJ

by Edoardo ''Dado'' Marcora

• Install ImageJ by extracting ij131.zip to 'C:\ImageJ' (Note: When extracting the zip files make sure you preserve folder information)
• Install Jython
  • Download jython-21.class and start installer by typing 'C:\ImageJ\jre\bin\java -cp . jython-21' in a command window assuming your current working directory is where you downloaded the jython-21.class file
  • Follow instructions and install Jython in 'C:\Jython21\'
• Replace 'Target' property of ImageJ shortcut with 'C:\ImageJ\jre\bin\javaw.exe -mx80m -cp ij.jar;jimi.jar;C:\Jython21\jython.jar; ij.ImageJ'
• Install Jython plugin by extracting jython_plugin.zip to 'C:\ImageJ\plugins\Jython' (Note: When extracting the zip files make sure you preserve folder information)
• Add 'C:\ImageJ' and 'C:\Jython21' to system path
• Extract this to 'C:\Jython21'. If asked, confirm replacing files
• To test the installation, extract this to 'C:\ImageJ\plugins\Jython', then:
  • run ImageJ
  • select menu Plugins>Jython>Jython Editor
  • select menu File>Open and open 'C:\ImageJ\plugins\Jython\HelloWorld.py'
  • click Evaluate. You should see a dialog box saying 'Hello World!'
  • quit ImageJ
  • open command window and goto 'C:\ImageJ\plugins\Jython'
  • type 'jythonc _HelloWorld.py'
  • exit command window
  • run ImageJ
  • select menu Plugins>Compile and Run...
  • open 'C:\ImageJ\plugins\Jython\_HelloWorld.java'
  • disregard the warning... you should see a dialog box saying 'Hello World!'
  • restart ImageJ
  • select menu Plugins>Jython>HelloWorld... you should see a dialog box saying 'Hello World!' w/o warnings.
• Open 'C:\ImageJ\plugins\Jython\HelloWorld.py' in your favorite text editor to get a glimpse at how to write ImageJ plugins using Jython.
• Have fun!!! :)

Please do not hesitate to contact me (marcora at caltech.edu) if you have any question, comment, or suggestion.