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mainpages:courses:basiccourse_preparation [2018/09/24 04:35]
kota [Preparation before Coming to the basic Course]
mainpages:courses:basiccourse_preparation [2019/01/31 04:11] (current)
kota
Line 4: Line 4:
  
   - Installation / Upgrading of Fiji (ImageJ).   - Installation / Upgrading of Fiji (ImageJ).
 +  - Install plugins using the Fiji updater and Update Sites. ​
   - If you have a problem, write an email to Kota.   - If you have a problem, write an email to Kota.
        
Line 17: Line 18:
 go to the Fiji download page:\\ go to the Fiji download page:\\
  
-http://fiji.sc/Downloads+https://imagej.net/Fiji/Downloads
  
 Download the latest one, whichever fits your OS. \\ Download the latest one, whichever fits your OS. \\
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 **step 2. Upgrading**\\ **step 2. Upgrading**\\
-Launch Fiji.  ​Do  [Help -> Update ​Fiji...]. You might need to restart ​and update several times, as updater ​itself is updated ​first, restart, then plugins+Launch Fiji.  ​From the menu, select ​ [Help -> Update...]. ​Fiji checks the status by comparing with the newest files in the download server ​and it takes 30 seconds or so to check this. Then A window titled "​ImageJ ​updater" opens (see below) with a list of files that need to be updated.
  
 +{{ :​mainpages:​courses:​imagejupdator2019.png?​400 |}}
  
-/* +If nothing is listed, just close the window because your Fiji is at the latest status. If you see the list like the image shown above, then click "Apply Changes"​ button. Fiji will start downloading newer files, and then when completed, it will ask you to restart Fiji - so please restart.  
-===== 2. Installing ​plugins ===== + 
-*/+You might need to restart and run the updater two times, as updater itself sometimes needs to be updated first before other things. ​  
 + 
 + 
 +===== 2. Install ​plugins ===== 
 + 
 +From the Fiji jmenu bar, select [Help > Update...]  
 +  ​The window "​ImageJ updater"​ opens.  
 +  * In that window, click the button "​Manage update sites" at the bottom-left.  
 +  * Another window called "​Manage Update Sites" opens. From the list of update sites, tick "​CMCI-EMBL"​.  
 +  * Depending on the workshop program, I will ask you to install more plugins. In that case, please also tick update sites that I will tell you to install. Such as: 
 +    * "​IJPB-plugins"​ (MorpholibJ) 
 +    * "​MosaicToolsSuite"​ (this includes Particle Tracker 2D/3D) 
 +  * After ticking required update sites, close the "​Manage update sites" window by clicking the button "​close"​.  
 +  * Back to the "​ImageJ updater"​ window, click the button "apply changes"​ at the bottom. It takes a while to download additional files. When completed, you will be asked to restart Fiji - so quit Fiji, and relaunch Fiji. Check the menu and there should be a new menu item "​EMBL"​.
  
 /* /*
mainpages/courses/basiccourse_preparation.1537788920.txt.gz · Last modified: 2018/09/24 04:35 by kota