Installation

cellclass is part of the omero-screen monorepo workspace. It is installed automatically when you run uv sync from the repository root.

git clone https://github.com/Helfrid/omero-screen.git
cd omero-screen
uv sync --dev
source .venv/bin/activate

The unified cellclass command provides all CellClass workflows; run cellclass --help to see its subcommands, or browse the generated CLI reference for the full command tree. Existing cellclass-* entry points remain available as compatibility aliases during the migration.

Weights & Biases

Training runs are logged to Weights & Biases. Set up your credentials once:

wandb login

Visit https://wandb.ai/authorize, log in, and paste the API key when prompted. The key is saved to ~/.netrc and persists across sessions and on the Artemis cluster. Verify the setup with:

wandb status

By default, runs log to the cellclass project in your own W&B workspace — no shared credentials needed. To collaborate with a team, pass --entity <team> to cellclass train (e.g. --entity hocheggerlab), then share the project via the W&B interface.