====== Bioimage Analysis Basics using ImageJ @Stuttgart ======

===== Date =====

Jan 21th (T), 22th (W) & 23th (T) 2020

===== Introduction =====

This **three-day introductory workshop** teaches the basics of digital image processing and analysis for biological / biomedical studies. The goal of the workshop is that participants acquire basic knowledge and technique for measurements using image data. 

Participation is most fruitful for learners who are conducting biological or medical research and are already using or are planning to use (light) microscopy for quantification purposes.

Participants should bring their own laptops. Please contact me in case this is not possible for you. Instructions on how to properly install and configure ImageJ will be provided before the workshop.

===== Location =====

The Bin-BW ImageJ workshop will take place at (TBA).

A detailed agenda is listed in the table below.

===== Workshop trainer =====

Kota Miura (kotapub@gmail.com), Freelance Bioimage Analyst & Vice Chair, [[http://eubias.org/NEUBIAS/|NEUBAIS (The Network of European Bioimage Analysts)]]

===== Learning Resources =====

  * http://wiki.cmci.info/documents/ijcourses
    * [[https://zenodo.org/record/51511|Basics of Image Processing and Analysis]]
    * [[https://zenodo.org/record/30267|Macro Programming in ImageJ]]
  * [[http://bit.ly/BIAS-book|Bioimage Data Analysis, 2016, Wiley]]
  * [[https://www.springer.com/gp/book/9783030223854|Bioimage Data Analysis Workflows, 2020, SpringerOpen]]
  * [[https://github.com/cmci/HTManalysisCourse|High-Throughput Image Screening using ImageJ]]

===== Preparation before coming =====

1. Please download Fiji from the following URL. 
  * https://imagej.net/Fiji/Downloads

2. Start Fiji, then in the menu [Help > Update...] 
  * A 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". 
  * Close the "Manage update sites" window by clicking the button "close". 
  * In 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".
  * More plugins to be installed will be announced later (using the update sites function, like explained above).   


===== Schedule =====

The schedule below may change depending on the progress, but the order of topics will mostly be kept as it is listed. 

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