# Image Processing and Analysis @EMBL

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### Index

 RT @Vofnfiji: KymographBuilder : Yet Another Kymograph Fiji plugin: Presentation. KymographBuilder is Yet Another Kymograph ... https://t.c … About 4 days, 20 hours ago by: Kota Miura (@cmci_) R.I.P https://t.co/EPcvfizeig About 1 week, 1 day ago by: Kota Miura (@cmci_) RT @CNRS_CFE: Stage de #formation "Analyse d'images automatisée avec #ImageJ et ICY" du 30/05 au 01/06 >>> https://t.co/J3BZrZvQ3z https://… About 1 week, 2 days ago by: Kota Miura (@cmci_) ... note that this UCL position sounds like an bioimage analyst position, not a bioinformatician. About 1 week, 2 days ago by: Kota Miura (@cmci_) RT @kvjanos">kvjanos: #Bioinformatics Research Associate job @ucl with #ImageJ and #RProject/#RStats/#R by @kvjanos">kvjanos on @LinkedIn https://t.co/PzaDi7 … About 1 week, 2 days ago by: Kota Miura (@cmci_) RT @ctrueden: #imagej news post: "Writing ImageJ2 Plugins: A Beginner's Perspective" by Karl-Heinz Kunzelmann, for aspiring devs. https://t… About 1 week, 3 days ago by: Kota Miura (@cmci_)

# Bioimage Data Analysis

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.

The book has been released as an open access textbook with the kind support of Olympus. It is available via download from this link: http://bit.ly/BIAS-book

# CMCI ImageJ Course Textbooks

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.

## Basics of Image Processing and Analysis

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).

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

## Macro Programming in ImageJ

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
• File I/O
• Secondary Measurements
• Using Javascript

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

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

### syntax highlighter

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:

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

## Misc

Textbooks have been used for teaching in following countries:

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

## Discussion

, 2013/07/10 15:41

sir, i would like to know wether it can be used in measuring bone density as done by ct ??

, 2014/04/01 08:16

Hello sir,i am tried a lot with Image J to quantifying the IHC images, but unable to estimate ,can you suggest the proper way for this.

, 2014/04/02 13:16

Sir,Can we find the measurement of Trichomes on the plant stems or leaves?Bold Text

, 2014/05/21 22:57

Hello, I am trying to use the batch processing to process a group of images with a macro that I recorded that allows me to make a substack and then do a z projection I have copied the macro I was recording below. However, when I try to evaluate the line that starts with “for” it gives me an error message that there is an undefined variable in line 1 and it shows <list>. Could you please help me figure this out or if you have any better suggestions I would really appreciate your input.

dir1 = getDirectory(“Choose Source Directory”); dir2 = getDirectory(“Choose Destination Directory”); list = getFileList(“dir1”) ; setBatchMode(true); for (i=0; i<list.length; i++) {

  showProgress(i+1, list.length);
open(dir1+list[1];
run("Make Substack...", "  slices=1-8");
selectWindow("Substack (1-8)");
run("Z Project...", "projection=[Max Intensity]");
saveAs("Tiff", "dir2+list[1];
close();
, 2014/05/26 22:53

Sofia, list = getFileList(“dir1”)

should be

list = getFileList(dir1)

, 2015/11/17 18:22