Recommended Installation of Miniforge3 and Cellpose3
Here you see, how to install Miniforge3 as well as Cellpose on Windows. Installation on MacOS is shown below.
Miniforge3 installation:

You find the page with the Miniforge3 installation instructions used in the following video here.
 
When you are in your Miniforge3 prompt in the base environment, please still run the following command to make the conda commands system wide usable. If you skip this step, you can later not use cellpose from within Fiji!

conda init


After running this command it will show some file paths displayed and most likely tells you to close the terminal window for this changes to take effect. So, close the command prompt and reopen it as seen before in the video.

Commands for cellpose 3.1.1.2 installation (see video below):

  1. First start your Miniforge3 command prompt from the Windows start menu
  2. Then run the following command (best copy-paste) in the command prompt one after the other. Easiest is, if you just copy the lines and paste them into your command prompt window to avoid typos.
conda env create -f https://www.biovoxxel.de/cellpose_installation/win_cellpose3.yml

  1. This will take a while until all packages are installed. Thereafter, it will indicate the following command to activate our newly installed cellpose3 environment.
conda activate cellpose3

  1. Now we test to start Cellpose with the command  
cellpose
 
General info on the Cellpose installation on Windows

For Cellpose, installation instructions are available on the Cellpose GitHub page

Some more info regarding potential issues can be found on the Cellpose page.

If you encounter further problems not discussed here please consult the image.sc forum for more help.

Getting cellpose to use the GPU on Windows (optional, not necessary for the course):

This part is not necessary doing the course and exercises but it might speed up calculation times. To make this really work you would also need to check that your graphic cards driver is up-to-date (not shown here).

pip uninstall torch

The following command will install cuda version 12.6 which might not work with all kinds of graphic cards. The video also shows where you find information on additional versions.

pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cu126
Here you see, how to install the Miniforge3 as well as Cellpose on MacOS.

Please check out the Miniforge3 online resources for installation

Disclaimer: We cannot guarantee that the installation on MacOS works exactly as shown in this video. 
 
Commands for cellpose 3.1.1.2 installation on MacOS (see video below):

  1. First start your command prompt from the Windows start menu
  2. Then run the following command (best copy-paste) in the command prompt one after the other. Easiest is, if you just copy the lines and paste them into your command prompt window to avoid typos.
conda env create -f https://www.biovoxxel.de/cellpose_installation/mac_cellpose3.yml

  1. This will take a while until all packages are installed. Thereafter, it will indicate the following command to activate our newly installed cellpose3 environment.
conda activate cellpose3

  1. Now we test to start Cellpose with the command  
cellpose
 
General info on the Cellpose installation on MacOS

For Cellpose, installation instructions are available on the Cellpose GitHub page

Some more info regarding potential issues can be found on the Cellpose page.

If you encounter further problems not discussed here please consult the image.sc forum for more help.