# 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:

``` bash
# 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:

``` bash
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

``` python
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

- Check out the [Quick Start Guide](quickstart.md) for basic usage
- Explore [Plot Types](plot_types.md) for available visualizations