The book “Bioimage Data Analysis (2016)” was released from Wiley as an open access textbook with the kind support of Olympus. It is available via download from this link: http://bit.ly/BIAS-book

In recent years, the focus in microscopy has changed from obtaining the correct image or sequence of images to the processing of said images. Therefore the field of image data analysis has become a crucial part of the experimental setup. So far the literature has not taken the image analyst into consideration, because the publications were either aimed at the computer science audience, i.e. focused on algorithm development, or at biologists, i.e. focused on the biological aspects. Kota Miura and his colleagues, from the EMBL in Heidelberg, have brought together their experiences to create a textbook that bridges this gap in the literature. All authors of the book have a track record of teaching courses about bioimage data analysis and their teaching materials became the building blocks of this book.

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.

DOI:10.5281/zenodo.51511

LaTex source

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/miura/ij_textbook1/issues?state=open

• makefile added with clean. PDF removed. (2016/05/16 16:13)
• s4 segmentation updated (2016/05/15 20:13)
• s3_filtering updated (2016/05/15 20:03)
• s2_intensity updated (2016/05/15 19:10)
• updates for BIAS2015 reflected, s1 Basics section. version 2.1.3 (2016/05/14 22:34)

DOI:10.5281/zenodo.30267

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/miura/ij_textbook2/issues?state=open

• origin merged (2017/11/06 23:57)
• pdf deleted (2017/11/06 23:55)
• variable section, added exercise answers from the book (2016/05/17 01:35)
• conditions, intro, still editing to be synced with the book (2016/05/17 01:34)
• macro recording synced to the book (2016/05/17 01:33)
• the aim synced to the book (2016/05/17 01:32)
• array application segmented ROI splitted to a file, added trivial fra… (2016/05/17 01:32)
• example of creating functions from a macro is now in a separate file (2016/05/17 00:13)
• string control sbsection added (2016/05/16 23:45)
• numerical array part synced with the book version (2016/05/16 23:45)

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

https://github.com/miura/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
• Greece
• Austria
• Switzerland
• Japan