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--- documents:ijcourses [2016/05/24 12:46] – external edit 127.0.0.1
+++ documents:ijcourses [2020/11/26 09:11] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
 ====== Bioimage Data Analysis ======
-{{:documents:olympus_leaderboard_728x90_now_ani.gif?direct&500|http://www.imaging-git.com/applications/bioimage-data-analysis-0?remove_param=true}}
+/*{{:documents:olympus_leaderboard_728x90_now_ani.gif|http://www.imaging-git.com/applications/bioimage-data-analysis-0?remove_param=true}}/*
-<quote>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. </quote>
+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]]
-The book has been released as an open access textbook with the kind support of Olympus. It is available via download from this link: [[http://bit.ly/BIAS-book]]
+{{ :media:biasvookcover.png?200|}}
+<blockquote>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. </blockquote>
-====== CMCI ImageJ Course Textbooks ======
+====== 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.
@@ Line 17: / Line 20: @@
 ===== Basics of Image Processing and Analysis =====
-[[https://github.com/cmci/ij_textbook1/files/266515/CMCIBasicCourse201102Bib.pdf|{{ :documents:textbooks:textbookbasicfront.jpg?200}}]]
+[[https://zenodo.org/record/51511|{{ :documents:textbooks:textbookbasicfront.jpg?200}}]]
+[[http://dx.doi.org/10.5281/zenodo.51511|DOI:10.5281/zenodo.51511]]
+[[https://github.com/miura/ij_textbook1/releases|LaTex source]]
 Basic course aims at biological researchers to learn basic knowledge and handling of image data using ImageJ. The textbook covers following topics:
@@ Line 30: / Line 38: @@
 To works with example images, install CMCI sample image loader plugin downloadable [[http://cmci.embl.de/downloads/sampleimageloader|from this page]].
-If you want to contribute to the textbook, you could fork the textbook project from its [[https://github.com/cmci/ij_textbook1|github page]] and work on it. You could then request a pull to me.
+If you want to contribute to the textbook, you could fork the textbook project from its [[https://github.com/miura/ij_textbook1|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
+https://github.com/miura/ij_textbook1/issues?state=open
 ==== update log ====
-{{rss>https://github.com/cmci/ij_textbook1/commits/master.atom 5 date 48h}}
+{{rss>https://github.com/miura/ij_textbook1/commits/master.atom 5 date 48h}}
 ===== Macro Programming in ImageJ =====
-[[https://github.com/cmci/ij_textbook2/blob/master/CMCImacrocourse.pdf?raw=true|{{ :documents:textbooks:textbookmacrofront.jpg?200}}]]
-<html><a href="http://dx.doi.org/10.5281/zenodo.30267"><img src="https://zenodo.org/badge/doi/10.5281/zenodo.30267.svg" alt="10.5281/zenodo.30267"></a><br></html>
+[[https://zenodo.org/record/30267|{{ :documents:textbooks:textbookmacrofront.jpg?200}}]]
+[[http://dx.doi.org/10.5281/zenodo.30267|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:
@@ Line 59: / Line 70: @@
 To works with example images, install CMCI sample image loader plugin linked for downloadable [[http://cmci.embl.de/downloads/sampleimageloader|from this page]].
-If you want to contribute to the textbook, you could fork the textbook project from [[https://github.com/cmci/ij_textbook2|github page]] and work on it. You could then request a pull to me.
+If you want to contribute to the textbook, you could fork the textbook project from [[https://github.com/miura/ij_textbook2|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
+https://github.com/miura/ij_textbook2/issues?state=open
 ==== recent updates ====
-{{rss>https://github.com/cmci/ij_textbook2/commits/master.atom 10 date 48h}}
+{{rss>https://github.com/miura/ij_textbook2/commits/master.atom 10 date 48h}}
 ==== syntax highlighter ====
@@ Line 73: / Line 83: @@
 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
+https://github.com/miura/ImageJMacro_Highlighter
 With Vim, the script also allows auto-completion of commands.