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EMBL BioImage Data Analysis

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Timeline of @cmci_

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Miyo Terao Morita showing analysis of gravitropism using centrifuge microscope they newly developed. I only know… https://t.co/Atj9E4QJAY
About 10 mins, 54 secs ago by: Kota Miura (@cmci_)

cmci_ avatar

@KeikoUTorii ... which then became the cover page of Development cell. convincing. https://t.co/XBgiqJpHog
About 1 hour, 8 mins ago by: Kota Miura (@cmci_)

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@KeikoUTorii model-based hypothesis lead to experiment results with single guard cell development or multiple >2 gu… https://t.co/oGhh4NJMPh
About 1 hour, 15 mins ago by: Kota Miura (@cmci_)

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now, @KeikoUTorii on stomata development - how very specific cell fate decisions are made, with proper spacing bet… https://t.co/XoR8tpB5WR
About 1 hour, 32 mins ago by: Kota Miura (@cmci_)

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@YvonJaillais talk on nanoclustering of ROP6, great analyses using various approaches to assess protein mobility… https://t.co/WHrzBsWTYJ
About 1 hour, 48 mins ago by: Kota Miura (@cmci_)

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RT @haesleinhuepf: I need to add this one, because I believe in the power of beautiful data. Same optics, just earlier stage in development…
About 13 hours, 20 mins 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

LaTex source

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: 2018/07/12 02:57 by kota