The following commands successfully installed Cellprofiler into an up to date Arch Linux system running GNOME in January 2024. This guide assumes you have an AUR helper such as yay installed - if not see https://github.com/Jguer/yay.

At this time, Arch ships with the most recent python version (3.11), however this is not supported yet by Cellprofiler. We need to install an earlier version of Python - 3.8 (tested, working) or 3.9 (not tested but believed to be working).

We also need an up to date java JDK development environment - make sure to install the full JDK, the JRE is not enough as it doesn't contain the javac compiler required to build the python-javabridge cellprofiler dependency.

Installation

Cellprofiler

yay jdk-openjdk

yay python38

python3.8 -m venv cellprofiler

source cellprofiler/bin/activate

pip install numpy wheel

pip install cellprofiler

Run the program with:

cellprofiler

We can follow this up by installing Cellprofiler Analyst:

Cellprofiler Analyst

python3.8 -m venv analyst

source analyst/bin/activate

pip install wheel pandas seaborn scikit-learn python-javabridge verlib python-bioformats

cd analyst

git clone https://github.com/CellProfiler/CellProfiler-Analyst.git

cd CellProfiler-Analyst

pip install .

And we can run the program with:

python3.8 CellProfiler-Analyst.py

Running the programs

To run both programs in the future, ensure you have activated the relevant virtual environment by going back to your home directory cd then running the respective commands, either:

source cellprofiler/bin/activate then cellprofiler for Cellprofiler, or

source analyst/bin/activate then python3.8 CellProfiler-Analyst.py for Cellprofiler Analyst.