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EMBL BioImage Data Analysis 2013 EMBL BioImage Data Analysis 2014

EuBIAS2013, Barcelona


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Timeline of @cmci_

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RT @Ng_Dave: Your graph for the day: “Life satisfaction” plotted against “nerds” or “most people.” http://t.co/NW4XCtbQg4 http://t.co/zqDSO
About 15 hours, 43 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @ManuelTHERY: Willy Supato ( 117 @ESPCI_Alumni) wrote a great review in NatureRevMCB about modern 3D imaging of embryo development! http…
About 1 day, 5 hours ago by: Kota Miura (@cmci_)

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@cortig @labmonkeyW If you want to avoid selecting a command from the deep menu tree with cluttering, use command finder (shortcut: L).
About 1 day, 9 hours ago by: Kota Miura (@cmci_)

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@cortig #ImageJ has about 500 commands, #Fiji has about 900. If you are satisfied with 500, I think it's OK.
About 2 days ago by: Kota Miura (@cmci_)

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@cortig I would say script editor is really great, which is available only in #Fiji.
About 2 days ago by: Kota Miura (@cmci_)

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RT @cortig: Can anyone tell me how #Fiji is better than #ImageJ? I fail to see the advantages at this point :-|
About 2 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

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