Installation

Requirements

  • Python 3.12, 3.13 or 3.14
  • OMERO Screen installation (for full pipeline integration)
  • Access to screening data in CSV format or cellview database

Install from Source

Since OmeroScreen Plots is part of the omero-screen monorepo, the recommended installation method is through the main project:

# Clone the repository
git clone https://github.com/Helfrid/omero-screen.git
cd omero-screen

# Install using uv (recommended)
uv sync --dev
source .venv/bin/activate

Standalone Installation

If you only need the plotting functionality:

cd packages/omero-screen-plots
uv pip install -e .

Dependencies

OmeroScreen Plots requires the following main dependencies:

  • pandas: Data manipulation and analysis
  • matplotlib: Core plotting functionality
  • seaborn: Statistical visualizations
  • numpy: Numerical operations
  • scipy: Statistical tests
  • scikit-posthocs: Post-hoc statistical tests

All dependencies are automatically installed with the package.

Verify Installation

import omero_screen_plots
print(omero_screen_plots.__version__)

Troubleshooting

Import Errors

If you encounter import errors, ensure that: 1. You’re in the correct virtual environment 2. The package is installed in editable mode (-e) 3. Your Python path includes the package directory

Missing Dependencies

Run uv sync to ensure all dependencies are installed correctly.

Next Steps