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EMBL BioImage Data Analysis



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RT @biomicugm: Topics: Biostatistics, computational evolutionary biology, computational genomics and proteomics, graph models, image analys…
About 4 days, 16 hours ago by: Kota Miura (@cmci_)

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RT @JustinMCrocker: We are looking for an interdisciplinary EIPOD postdoc to join our group @EMBL! Potential projects with @Eileen_Furlong,…
About 4 days, 16 hours ago by: Kota Miura (@cmci_)

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RT @BioImagingUK: This maybe of interest to the @NEUBIAS_COST @openmicroscopy communities #imageAnalysis #imagingScientist
About 4 days, 16 hours ago by: Kota Miura (@cmci_)

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RT @BioImagingUK: Software developer position on large image data analysis - working closely with the lab of @bayraktar_lab @sangerinstitut…
About 1 week, 2 days ago by: Kota Miura (@cmci_)

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RT @AssafZaritsky: Modeling the interplay of lamellipodial motion and the intercellular actomyosin cable during epithelial wound healing h…
About 1 week, 2 days ago by: Kota Miura (@cmci_)

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RT @jytinevez: @florianjug says be careful when using #CARE for intensity based quantification; CARE restoration is like a non linear trans…
About 1 week, 4 days 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