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EMBL BioImage Data Analysis

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cmci_ avatar

RT @qiita_rss: kouichi-c-nakamura がQiitaに投稿しました. How to Use ImageJ-MATLAB matlab・ImageProcessing・ImageJ https://t.co/yD0RKXOWDY
About 1 day, 2 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @experimentIV: I 💜showing new students how ImageJ macros work. They show you the buttons they've been repeatedly clicking for a couple o…
About 1 day, 2 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

@Morimagic @EuroBioImaging correct link: International Job Shadowing Program https://t.co/gEmezh45Zg
About 1 day, 2 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @ManuelTHERY: Here is a microtubule before and after this: https://t.co/mVIt9aQTzw Think about all proteins and functions associated to…
About 1 day, 2 hours ago by: Kota Miura (@cmci_)

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RT @experimentIV: This is a great idea and I'm glad it's coming https://t.co/N2pe9sy59r
About 2 days, 2 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @UAM_Medicina: Image analysis in Biomedical Research Seminar. Friday, 2 February 2018. The aim of the seminar is to provide the theoret…
About 2 days, 15 hours ago by: Kota Miura (@cmci_)
documents:ijcourses

Bioimage Data Analysis

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.

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

textbookbasicfront.jpg

DOI:10.5281/zenodo.51511
PDF download

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

update log

Macro Programming in ImageJ

textbookmacrofront.jpg

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

recent updates

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:

https://github.com/miura/ImageJMacro_Highlighter

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
documents/ijcourses.txt · Last modified: 2017/06/06 18:17 by kota