Advanced Microscopy – Machine & Deep Learning

Hi Students of the advanced Microscopy Course,

For this course we will use QuPath 0.3.2 (with the Stardist Plugin)

Please familiarize yourself with QuPath a bit. A good start is looking at the video tutorials #1: https://www.youtube.com/c/qupath

Install QuPath and download Examples

https://qupath.github.io
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: https://github.com/qupath/qupath/releases/tag/v0.3.2)
On a MAC you have to hold down the left SHIFT key and click the install package and allow it to install.

When done installing QuPath download the course data here: QP-ML-Course.zip

Unzip this file and find the “project.qpproj” file in the “ML-DL-Data-Examples/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.

Install Stardist 

You also have to install the Stardist extension. (https://github.com/qupath/qupath-extension-stardist)

To install the StarDist extension, download the latest qupath-extension-stardist-0.3.2.jar file from releases and drag it onto the main QuPath window.

When selecting the “Installed extensions” menu item in the “Extensions” Menu, you should see “StarDist  extension (0.3.x) “.

Optionally install Cellpose and the QuPath Cellpose Plugin
We will not use this in the course practical but I will cover it in the talks
Installing Cellpose requires a Conda Python Environment. For detailed installation intructions read:
Instead of Anaconda (as is shown on the install instruction of Cellpose), you can also (or maybe better) install Miniconda:
  1. Download Miniconda, install and it, be sure to check both checkboxes when running set-up)
    https://docs.conda.io/en/latest/miniconda.html
  2. On the user command-line (run cmd.exe) run these commands in this order!: 
    1. conda create --name cellpose
    2. conda activate cellpose
  3. Follow the instructions on the Cellpose Github Site.
  4. Install the QuPath Cellpose Extension (like the Stardist Extension)
    https://github.com/BIOP/qupath-extension-cellpose/releases
  5. Do not forget to set the settings of this plugin to Conda Env: cellpose and cellpose
  6. Cellpose is very slow without a GPU. If you have a Nvidea GPU and run Windows or Linux folow the instruction op de Cellpose site to install GPU support.

Here a video of my install on Windows 11. As mentioned above the installation of QuPath can ask more questions because of security settings of your computer. In the video you do not see them.

 

Click here for three video’s of examples of segmenting and classifing cells with the use of QuPath and Stardist