For this course we will use QuPath 0.3.2, Stardist and Cellpose
- QuPath: https://www.nature.com/articles/s41598-017-17204-5
- Stardist: https://arxiv.org/abs/1806.03535
- Cellpose: https://www.biorxiv.org/content/10.1101/2020.02.02.931238v2
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 (with Stardist) and download Examples
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.
You also have to install the Stardist extension. (https://github.com/qupath/qupath-extension-stardist)
- Start QuPath first (at first start you have to set the memory limit, by default is half of system memory, it is better to make this higher)
- To install the StarDist extension, download the latest
qupath-extension-stardist-0.3.jarfile from releases and drag it onto the main QuPath window.
When done 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. When selecting the “Installed extensions” menu item in the “Extensions” Menu, you should see “StarDist extension (0.3.0) “.
- Download Miniconda, install and it it to the PATH (check both checkboxes when running set-up)
- On the user command-line (run cmd.exe) run these commands in this order!:
conda create --name cellpose
conda activate cellpose
conda install pytorch cudatoolkit=11.3 -c pytorch (optional but strongly recommended if you have a Nvidia GPU)
pip install cellpose[gui]==1.0.2
cellpose (this will run cellpose once , which is needed!)