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

RT @DrAndrewBurgess: #Mitosis Saturday. Absolutely stunning picture of a cell in #anaphase. http://t.co/qjji3e0zzi
About 1 day, 14 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

agree. 2007. RT @drdanwhite: @MyBioTechniques the imagej article totally fails to mention all the new exciting progress of ij2 and Fiji...
About 1 day, 19 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @christlet: QuickSOFI: a GPU-based ImageJ plugin for SOFI super-resolution image analysis (pdf link on page, but plugin itself?) http://…
About 1 day, 19 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @1024jp: Update ImageJ Macro syntax definition for CotEditor. 1024jp/ImageJ-coteditor https://t.co/6QoeAx86sm
About 4 days ago by: Kota Miura (@cmci_)

cmci_ avatar

on statistics abuse, many people should read... http://t.co/AvgfxOX5Vg via @fronori & @loveacidjazz
About 6 days, 13 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

There seems to be no guideline for the reuse of Nature article's supplementary materials ... is it free?
About 1 week, 5 days 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

, 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)

Enter your comment
BKZQX