Pom installation

Pom is a companion package to easymode. Once you've segmented many different things with easymode (or Ais, or any other segmentation tool), you can use Pom to organise and curate the data.

Pom is installed together with easymode (pip install easymode), so there is nothing extra to install. To install Pom on its own, use pip install pom-cryoet.

Pom browser app

The browser app (pom browse) needs streamlit, which is not installed by default because it conflicts with tensorflow's protobuf requirement. To use the app, install streamlit first and then protobuf:

pip install streamlit==1.56.0 streamlit-aggrid
pip install protobuf==3.20.0

pip will warn that tensorflow or streamlit is incompatible with this protobuf version. Ignore that; it works.

3D visualization

Pom uses OpenGL and glfw for 3D visualization. The pom render command can only be run on a system that supports these, so headless servers can cause issues. On our cluster it works fine as long as we connect with X11 forwarding: ssh -X user@entrypoint, or srun --x11 --pty -p agpu --gres=gpu:4 bash when connecting to a GPU node.