paquo should work with any QuPath version starting with 0.2.0 or higher. Follow Paquo Issue #19 to be notified when we’re starting to work on adding QuPath version tests to our CI.

Install paquo

paquo is installable via pypi. To get the newest stable version, run:

user@computer:~$ pip install paquo

You can also install it via conda:

user@computer:~$ conda install -c conda-forge paquo

Install QuPath

paquo requires a working QuPath installation. Please follow the instructions here on how to install QuPath on your system. As long as you install in the default directory paquo should be able to find it without any additional configuration. If you have installed QuPath in a different location, you need to configure paquo so that it can find it. Check out the Configuration section to learn more.


For your convenience we added a commandline option to the paquo commandline interface to simplify installing a specific version of QuPath. After having installed paquo, run:

user@computer:~$ paquo get_qupath --install-path ./some-directory 0.3.2

This will download the specified version and extract it to ./some-directory. It also prints some instructions on how to use paquo with the downloaded QuPath.

Install paquo’s dev environment

While we’re rushing towards the next release, we’re constantly changing and improving the way paquo operates. If you think you have what it takes to live on the bleeding edge of paquo development, the easiest way is to make sure you have git and conda and conda-devenv installed and then run:

user@computer:~$ git clone
user@computer:~$ cd paquo
user@computer:paquo$ conda devenv --env PAQUO_DEVEL=True --print > environment.yml
user@computer:paquo$ conda env create -f environment.yml

This will create a paquo conda environment with everything you need to get started. It installs a special conda-packaged QuPath that we’re currently using to develop paquo and also installs all the other things required. You should now be able to run:

user@computer:paquo$ conda activate paquo
(paquo) user@computer:paquo$ pytest

And you should see that all the tests pass ❤️