Tweet CMCIlogo

Image Processing and Analysis @EMBL

Trace: ijcourses


|

Index

Top
Mission
CMCI Seminar
Courses
Documents
Downloads
GitHub
Links
Links - video
Calendar
Bioclips
Weblog
Hand Picked Papers
Sitemap
Discussions
Change log


EMBL BioImage Data Analysis 2013 EMBL BioImage Data Analysis 2014

EuBIAS2013, Barcelona


Contact
CMCI Alumni
ALMF
EMBL Heidelberg
EMBL Intranet
Biophysics Journal Club


Timeline of @cmci_

cmci_ avatar

Introduction to Image Processing Using R http://t.co/HZy4tklojy
About 2 days, 3 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @JSchindelin: @cmci_ @labmonkeyW you should really send a mail with example images to imagej@list.nih.gov. The IJ community might help, …
About 2 days, 17 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

In fact, does not even have to be displayed. @CAYdenberg: ... all #ImageJ does is read, display, and write them. http://t.co/7Y9rvtvs8N
About 2 days, 21 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @jmutterer: @cmci_ definitely possible. I'll put what I have so far on github. Thanks for RT
About 3 days, 4 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

@jmutterer looks pretty useful! It would be great to have "run macro" or "run jython" orts of command...
About 3 days, 5 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @jmutterer: Having fun playing with #ImageJ from #Galaxy http://t.co/pRJ3XYCoKq via @YouTube
About 3 days, 6 hours ago by: Kota Miura (@cmci_)

Meta

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

textbookbasicfront.jpg 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

update log

Macro Programming in ImageJ

textbookmacrofront.jpg 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

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/cmci/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

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

Enter your comment
UQBGH