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

cd && 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.

Troubleshooting

During pip install cellprofiler; python-javabridge failed to build; javac not found

Check that you have the jdk-openjdk AUR package installed as that package provides javac. If you have it already, you probably have or had an alternative java environment installed that is conflicting at the system level. Check the environments Arch has access to with

archlinux-java status

Then set the correct default with

sudo archlinux-java set jdk-openjdk

You should be able to complete the cellprofiler pip installation now.

Starting cellprofiler gives ImportError: [some library]: cannot open shared object file: No such file or directory

These errors occur because cellprofiler is expecting a system library that was there when cellprofiler was originally built, but which is no longer available to it (probably because of a system update).

You'll need to go through the install process again, so that cellprofiler builds whilst linking to the current system libraries. There may be a way of fixing the issue by diving into the files in the existing python environment, but this way worked for me.

Important: This will delete your cellprofiler application and virtual environment, but won't touch your images, exports, or program settings (assuming you've stored those elsewhere in your home directory (which would generally be the case).

First, make sure you're in the virtual environment.

cd && source cellprofiler/bin/activate

delete the existing pip packages so that a new build will be triggered when you reinstall cellprofiler.

pip cache purge

Then, delete your existing cellprofiler virtual environment.

cd && rm cellprofiler/*

rmdir cellprofiler

Then, you can go back to the installation instructions above (starting at the python3.8 -m venv cellprofiler line) to rebuild your cellprofiler application and associated packages.

Using GNOME DE, and unable to click on any elements in the main window

This seems to be a bug with the linux version of python or wxwidgets on gtk, but only under a wayland session. You can log out and switch to an X11 session in order to work around this issue until it is fixed upstream.