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EMBL BioImage Data Analysis



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RT @teofilo_breno: @TheCrick Biolmage Analysis Symposium. @infabic. #CBIAS2020 #BioImageAnalysis #Microscopy
About 14 hours, 19 mins ago by: Kota Miura (@cmci_)

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RT @dgaboriau: Fascinating talk by Peter Horvath @hpke1980 on AI based segmentation, especially good for overlapping objects like nuclei.…
About 22 hours, 20 mins ago by: Kota Miura (@cmci_)

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A new data set of mouse embryo head published, #Neubias community @ zenodo
About 1 day, 10 hours ago by: Kota Miura (@cmci_)

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@digitalsreeni @sebisabs @Apeer_micro Yes, and It would be great if APEER workflow allows minting with DOI - so a…
About 1 day, 22 hours ago by: Kota Miura (@cmci_)

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RT @LarryMattYork: If you'd like to learn more about RhizoVision Explorer and its capabilities, you can view and download the manual from t…
About 1 day, 22 hours ago by: Kota Miura (@cmci_)

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RT @DD_Wen_: Image Processing with Keras in Python: Learn powerful techniques for image analysis in Python using deep learning and convolut…
About 1 day, 22 hours ago by: Kota Miura (@cmci_)

Bin-BW ImageJ Scripting Workshop: Heidelberg May, 2019


May 8th (Wed) and 9th (Thu), 2019


As part of the initiative Bin-BW (Bioimage-Net Baden-Württemberg), the Math Clinic of the Heidelberg University and the Bioimaging Center of the University of Konstanz offers workshops in image analysis based on the open-source software ImageJ.

The two-day ImageJ scripting 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.

Workshop contents can be viewed in the following textbook: ImageJ Macro Language, Kota Miura


The Bin-BW ImageJ workshop will take place at Heidelberg University - BioQuant, Im Neuenheimer Feld 267, Room 41

The schedule is shown in the table below.


Carlo Bretta (
Ulrike Engel


Kota Miura (, Freelance Bioimage Analyst & Vice Chair, NEUBAIS (The Network of European Bioimage Analysts)


Registration Form

Deadline: April 29th, 2019

The maximum number of participants is 15. When there are more than 15 people applying, selection will be made based on the experience.

Registration Fee

20 euros. Accepted participants will be contacted for the payment.

Preparation before coming

1. Please download Fiji from the following URL.

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”.

3. Please set-up your WIFI connection in the campus (e.g. eduroam)


May 8th

  • 9:00 -12:00
    • Setting up
    • using script editor in Fiji
    • Hello World
    • Looping
    • assignments/answers
  • 13:30 - 16:00
    • Conditions
    • Arrays
    • GUI
    • assignments/answers

May 9th

  • 9:00 - 12:00
    • User-defined functions
    • string operations
    • File system IO
    • assignments/answers
  • 13:30 - 16:00
    • Machine Learning workflows
    • Constructing practical workflows
    • 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.

mainpages/courses/201905heidelberg.txt · Last modified: 2019/05/07 08:43 by kota