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EMBL BioImage Data Analysis



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RT @jytinevez: LimeSeg on bioRXiv: LimeSeg: A coarsed-grained lipid membrane simulation for 3D image segmentation
About 9 hours ago by: Kota Miura (@cmci_)

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Impressive and swift moderation @helenajambor !
About 2 days, 13 hours ago by: Kota Miura (@cmci_)

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RT @LuisDVerde: Now available as a #ggplot2 geom thanks to @naupakaz
About 2 days, 14 hours ago by: Kota Miura (@cmci_)

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RT @helenajambor: awesome, within 2 days .@naupakaz made a code publicly available for anyone wanting to make the half-and-half-plot FYI @…
About 2 days, 14 hours ago by: Kota Miura (@cmci_)

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RT @dgaboriau: Thread on data visualisation: ggplots, boxplots and violin plots
About 2 days, 19 hours ago by: Kota Miura (@cmci_)

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RT @christlet: SUSHI from Valentin Nāgerl lab allows super-resolution microscopy of neuronal morphology by STED imaging of extracellular sp…
About 2 days, 22 hours ago by: Kota Miura (@cmci_)

Preparation before Coming to the basic Course

Before you come to the course, there are several things you should do by yourself.

  1. Installation / Upgrading of Fiji (ImageJ).
  2. Download and install plugins.
  3. If you have problem, call Kota (ex 8404).


1. Installation of the newest version Fiji(ImageJ).

Please be ready with the newest Fiji installed in 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 second one just for the course.


step 1. Download Fiji (ImageJ)
go to the Fiji download page:

Download whichever fits to your OS (in all cases, download “continuous release”).

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…]. You might need to restart and update several times, as updater itself is updated first, restart, then plugins.

Do also [Help > Update ImageJ]. This updates the core ImageJ.

2. Downloading textbook and plugins

Course Textbook

Follow the link below, click the textbook image. Download of the textbook should then start. Depending on your preference, print out the text book and bring it along with you to the class.


Please install 5 plugins. Download a .jar or a .class file from the following links.

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.


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 use of the laptop is intensive during the course, the power supply often becomes problem. Bring down extension cable with multiple sockets if you could find it in your lab.

mainpages/courses/basiccourse_preparation.txt · Last modified: 2017/06/06 20:16 by kota