Course Data Analysis

Hi Students.

For this course we will use QuPath 0.3.0,  Fiji (+Stardist Plugin) and Ilastik


Fiji (ImageJ) + Stardist Plugin


Ilastik (Beta version 1.4)

Scroll down on the download page to: “Example data and projects” and download at least: “Small FIB/SEM stack”  example. (You can download more examples later if you want to try these)


On Windows run the downloaded MSI file, it will complain about not being verified, just allow it to install.
(Alternatively download the zip file, see:
On a MAC you have to hold down the left SHIFT key and click the install package and allow it to install.

You also have to install the Stardist extension. (

  1. Start QuPath first (at first start you have to set the memory limit)
  2. To install the StarDist extension, download the latest qupath-extension-stardist-0.3.jar file from releases and drag it onto the main QuPath window.

When done download the course data here:

Unzip this file and find the “project.qpproj” file in the “ML-DL-Data\QPP” folder. Drag it into the main QuPath window to open de project.
It will sometimes show a dialog while loading the project, because it cannot locate the data files (images). It suggest most of the time correctly where the data files are (in the ML-DL-Data folder).

If everything is correct, you see the data files (images) on the left. When selecting the “Installed extensions” menu item in the “Extensions” Menu, you should see “StarDist  extension (0.3.0) “.

For the Stardist Google Colab Code (I will show this code during the course):

Make a copy in your own Google Drive if you want to play with the code.