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EMBL BioImage Data Analysis



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RT @teofilo_breno: @TheCrick Biolmage Analysis Symposium. @infabic. #CBIAS2020 #BioImageAnalysis #Microscopy
About 13 hours, 53 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 21 hours, 54 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, 9 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, 21 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_)
Algorithm FRAP Fiji ImageJ ImageJ Plugin ImageJ Plugin 3Dviewer Imaris Java Javascript Python R added 201904 Freiburg bias blog dokuwiki fiji google imagej java libraries matlab meetings neubias news papers python references software webadmin

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Kota Miura, Ph.D.

Bioimage Analyst



Workshop: Basics of Bioimage Analysis using ImageJ


Kota Miura (Ph.D., Bioimage Analyst)



Wing-Kee Lee, B.Sc., Ph.D.
Assistant Professor
Institute for Physiology, Pathophysiology & Toxicology
Department of Medicine, Faculty of Health
University of Witten/Herdecke

Place and Time

Place: FEZ (großer Saal), Alfred-Herrhausen-Straße 50, 58455 Witten
Date & Time: September 24th (10:00-18:00) & 25th (9:00-17:00), 2020


Slides will be provided to you after the workshop.

Please install Fiji and plugins in your machine. Instructions are written in the page below.


Day 1: 24 September (Thu), 2020

Time Topic
10:00 - 11:00 Introduction
11:00 - 11:30 COFFEE BREAK
11:30 - 12:30 From Images to Numbers
12:30 - 13:30 LUNCH BREAK
13:30 - 15:30 From Numbers to Images
Multi-Dimensional Data
15:30 - 16:00 COFFEE BREAK
16:00 - 18:00 Region of Interest and Segmentation
Pre- & Post-processing for a better segmentation
How filters work, Usage of Filters

Day 2: 25 September (Fri), 2020

Time Topic
09:00 - 10:00 Measurements: Counting and Locating Dots
10:00 - 10:30 COFFEE BREAK
10:30 - 12:30 Measurements: Lengths
Measurements: Area
Measurements: Volume
12:30 - 13:30 LUNCH BREAK
13:30 - 15:00 Batch Processing
Measuring Intensity Changes
15:00 - 15:30 COFFEE BREAK
15:30 - 16:30 Measuring Position Changes: Tracking Manually
Measuring Position Changes: Tracking Automatically
16:30 - 17:00 Answering to questions posted before the workshop

ImaegJ Macro Headless Limitations

There are two ways to run ImageJ “Headless”ly.

1. Real-Headless: running ImageJ without any display. 2. Pseudo-Headless: running ImageJ without physical display, but with a virtual display that is hidden - virtual frame buffer. xvfb-run command is often used for this purpose.

With the second method, you can run ImageJ macro just like you do with GUI. The speed of processing is similar to that you experience with normal GUI. With the first method, as there is no GUI drawing involved, the processing becomes much faster - but there are some problems. As some of the windows often used in ImageJ macro, such as ROI Manager and Results table cause “headlessexception” error and you will fail in the successful execution of that macro. (If you use xvfb-run, this does not happen).

There is some workaround as shown below.

ROI Manager

Don't use ROI Manager in a pure-headless environment. Instead, use Overlay function like the example below.

run("Blobs (25K)");
run("Analyze Particles...", "  show=Overlay");
newImage("Untitled", "8-bit ramp", 256, 254, 1);
for (i=0; i<Overlay.size; i++) {
  mean = List.getValue("Mean");
  print(i+"  "+mean);

Results Table

You can see the results table by saveAs(“Results”, path) command, but the renaming of the results table becomes impossible in the pure-headless environment. Avoid renaming, and instead, try to save the results table as soon as the results are filled in the table with a specific file name.

Bioimage Analysis Basics using ImageJ @Stuttgart


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


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.


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

A detailed agenda is listed in the table below.

Workshop trainer

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

Learning Resources

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”.
  • More plugins to be installed will be announced later (using the update sites function, like explained above).


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

Bioimage Data Analysis Workflow (2019) Springer

We now have a new book "Bioimage Data Analysis WOrkflow"published from Springer, topics of which are centered around bioimage analysis workflows. The book is open access - thanks to the support from COST Action.

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