Textbooks were first used in 2006 and then progressively updated since then. As the evolution of ImageJ seems to never stop, the textbooks will continue to be updated. Please come back to this page if you want to get the latest version.

Copyright is reserved and download is free for non-commercial purpose. If you want to use these textbooks for charged-courses or commercial purpose, please tell me so I can charge you :). If there is any chance please acknowledge the author whenever you could.

Basic course aims at biological researchers to learn basic knowledge and handling of image data using ImageJ. The textbook covers following topics:

• Basics of Basics
• Intensity
• Filtering
• Segmentation
• Analyzing Time-Series

Click the textbook image to download the PDF (app. 5Mb., 156 pages).

To works with example images, install CMCI sample image loader plugin downloadable from this page.

If you want to contribute to the textbook, you could fork the textbook project from its github page and work on it. You could then request a pull to me.

Otherwise, if you find mistakes (I know there should be a lot), just post your suggestion as a “new issue” at

https://github.com/cmci/ij_textbook1/issues?state=open

• acknowledgement added with Sebastien (2013/05/02 03:47)
• projection part, changed to projection of time series. (2013/05/02 03:46)
• pdf update (2013/05/02 03:44)
• added more on multidimensional images and visualization, stack editing, comamnd finder, (2013/05/02 03:44)
• new figures (2013/05/02 03:41)

Macro programming course primarily aims at making biologist's life easy by scripting iterative tasks. By writing ImageJ macro, you could automate many time-consuming tasks. A glance of textbook chapters:

• Why do we write macro?
• Basics
• Conditions and Loops
• Advanced Macro Programming
• File I/O
• Secondary Measurements
• Using Javascript

Click the text book image to download the textbook (ca. 1.6Mb, 126 pages).

To works with example images, install CMCI sample image loader plugin linked for downloadable from this page.

If you want to contribute to the textbook, you could fork the textbook project from github page and work on it. You could then request a pull to me.

Otherwise, if you find mistakes (I know there should be a lot), just post your suggestion as a “new issue” at

https://github.com/cmci/ij_textbook2/issues?state=open

• added text manupilation sub section (2013/04/18 20:41)
• changes in the term 'function' and 'commands' (2013/04/18 14:08)
• updates associated with BIAS (2013/04/12 11:34)
• updates associated with BIAS (2013/04/10 04:20)
• line ending change (2013/04/09 19:06)
• updates with introduction (2012/11/16 02:29)
• dot animation macro updated (2012/11/16 01:47)
• spelling mistakes corrected (2012/11/15 19:25)
• updated code 20_76 added. 20_75 is not used anymore, but keep it as a good comparison of seeing difference after using new Array functions. (2012/05/16 15:09)
• Added array functions, and updated code 20_75 to 20_76. Code is simpler now with Array functions. (2012/05/16 15:07)

I recommend Fiji script editor for beginners to edit macro. But for those who prefers to use external editors, IJ macro syntax highlighter add-on for Vim, Notepad++(Windows) and CotEditor (OSX) are available at:

https://github.com/cmci/ImageJMacro_Highlighter

With Vim, the script also allows auto-completion of commands.

Textbooks have been used for teaching in following countries:

• Germany
• Finland
• Italy
• Spain
• Sweden
• Singapore
• Belgium
• Austria
• Switzerland
• Japan