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--- mainpages:courses:basiccourse_preparation [2012/02/03 14:38] – kota
+++ mainpages:courses:basiccourse_preparation [2019/01/31 11:49] – [INSTRUCTION] kota
@@ Line 3: / Line 3: @@
 Before you come to the course, there are several things you should do by yourself.
-  - Installation of Fiji (ImageJ).
+  - Installation / Upgrading of Fiji (ImageJ).
-  - Download course package.
+  - If you have a problem, write an email to Kota.
-  - If you have problem, call Kota (ex 8404).
 **Details: **\\
@@ Line 11: / Line 10: @@
 ===== 1. Installation of the newest version Fiji(ImageJ). =====
-Please be ready with the newest Fiji (ImageJ) installed in your laptop.
+Please be ready with the newest Fiji installed on your laptop. If you already have one installed, be sure to upgrade the software (see step 2). If you do not want to upgrade for whatever reason, just install the second one just for the course.
-**If you already have ImageJ in your machine, place a second Fiji(ImageJ) on desktop or somewhere** different from the one you have already. This is to avoid so called "class conflict" problem due to the redundant plugin.
 ==== INSTRUCTION ====
 **step 1. Download Fiji (ImageJ)**\\
-go to the Fiji download page\\
+go to the Fiji download page:\\
-http://pacific.mpi-cbg.de/wiki/index.php/Downloads
+https://imagej.net/Fiji/Downloads
-download whichever fits to your OS. \\
+Download the latest one, whichever fits your OS. \\
-Then install the program. In case of Windows, you just need to unpack the zip file and place the folder somewhere. In case of Mac OSX, double click the .dmg file and install it as usual.\\
+In Windows OS, you just need to unpack the zip file and place the folder on your Desktop. With Mac OSX, double-click the .dmg file and install it as usual (copy Fiji to Application folder).\\
 **step 2. Upgrading**\\
-Start Fiji.  Do  [Help -> Update Fiji...].
+Launch Fiji.  Do  [Help -> Update Fiji...]. You might need to restart and update several times, as updater itself is updated first, restart, then plugins.
 /*
-**step 3 Check ImageJ Version**\\
+===== 2. Installing plugins =====
-restart ImageJ. In the menu, do [help -> about ImageJ...].\\
-If you see "ImageJ **1.44f** (or larger)" your laptop is with the newest ImageJ.
 */
-===== 2. Downloading textbook, plugins and sample images. =====
+/*
-Please download zipped file from the download link I will send you.
+Please install 5 plugins. Download a .jar or a .class file from the following links.
+  * Sample Image Loader
+    * https://github.com/miura/CourseUtil/blob/gh-pages/target/EMBL_sampleimages-1.0.0.jar?raw=true
+  * Mosaic ToolsSuite (ParticleTracker)
+    * http://mosaic.mpi-cbg.de/Downloads/Mosaic_ToolSuite.jar
+  * Pure Denoise
+    * http://bigwww.epfl.ch/algorithms/denoise/
+  * Running ZProjector
+    * http://valelab.ucsf.edu/~nstuurman/IJplugins/Running_ZProjector.html
+  * Polynomial Fit
+    * http://www.optinav.com/Polynomial_Fit.htm
-name of the file is
+Then install plugins one by one, be selecting [Plugins > Install Plugins] in the Fiji menu and choose the file you downloaded. The plugin jar file could also be dragged and dropped in the Fiji menue bar to save it in the plugin folder.
-**course_files20120200.zip**\\
+*/
-... inside, there are two folders and a textbook PDF (I might send you this pdf separately).\\
+===== Optional: The Basic Course Textbook =====
-. Sample_Images\\
-containing image files we use in the course: copy it into your laptop. when expanded, size is about 290Mb.
-. Plugins\\
+If you want a textbook, follow the link below and click the textbook image. Downloading of the textbook should then start.
-ImageJ PlugIns we use in the course: please copy this folder under 'Plugin' folder or directory, inside ImageJ folder or directory\\
-. PDF\\
+http://cmci.embl.de/documents/ijcourses#basics_of_image_processing_and_analysis
-references.
-**Course Textbook**
+/*
+===== Misc =====
-Follow the link below, click the pdf in the file listing. You will see a new page with "view". Clicking it will start the downloading of the file. Depending on your preference, print out the text book and bring it along with you to the class.
+Please bring down power extension cable (for your laptop) for the course! Those of you with a laptop that works more than 2hours only with battery does not have to do this, but since the use of the laptop is intensive during the course, the power supply often becomes a problem. Bring down extension cable with multiple sockets if you could find it in your lab.
+*/
-[[https://github.com/cmci/ij_textbook1]]
-===== MiSC =====
-Please bring down power extension cable (for your laptop) for the course! Those of you with PC working without external supply for more than 2hours will be ok without. Since each of you use laptop full time during the course, its always that the power supply becomes problem. Bring down extension cable with multiple sockets if you could find it in your lab.