Nov 11th and 12th, 2019

The Bioimaging Center of the University of Konstanz offers workshops in image analysis based on the open-source software ImageJ, as a part of a new program of German Bioimaging “Rent-a-Trainer”.

This two-day ImageJ macro workshop teaches the ImageJ macro programming for biological / biomedical image analysis. The goal of the workshop is that participants acquire basic programming techniques for analyzing image data.

Participation is most fruitful for learners who are conducting biological or medical research and are already using (light) microscopy for quantification purposes, and also has some experiences in using ImageJ.

Participants should bring their own laptops. Instructions on how to install ImageJ is explained below.

The workshop will take place at the University of Konstanz, Room H308. The schedule is shown in the table below.

Dr. Kota Miura (kotapub@gmail.com), Freelance Bioimage Analyst & Vice Chair, NEUBAIS (The Network of European Bioimage Analysts)

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”.

• 10:30 -12:00
  • Setting up
  • using script editor in Fiji
  • Hello World
• 13:00 - 17:00
  • Looping
  • Conditions
  • Arrays
  • A bit more advanced techniques
  • assignments/answers

• 10:00 - 12:00
  • string operations
  • File system IO
  • assignments/answers
• 13:00 - 16:30
  • more applications: scripting machine learning based segmentation
  • assignments/answers

From time to time, with coffee breaks in between for both days. This will be not the exact schedule. It will be adjusted depending on the progress.