Installation

Prerequisites

  • Python 3.12, 3.13 or 3.14
  • Napari 0.6.2+ with Qt backend
  • Access to an OMERO server (5.x) with valid credentials
  • Segmented plate data on OMERO (nucleus/cell masks uploaded by the omero-screen pipeline)

Install from the Monorepo

The recommended way to install is from the omero-screen monorepo, which includes all packages:

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

This installs omero-screen-napari along with all workspace dependencies.

Standalone Install

If you only need the Napari widgets:

uv add omero-screen-napari

OMERO Connection

The widgets connect to OMERO using credentials from environment files. Create a .env.development (or .env) in the project root:

USERNAME=your_omero_username
PASSWORD=your_omero_password
HOST=your.omero.server.com

Select the environment with the ENV variable:

export ENV=development   # default
export ENV=production    # for production server

Verify Installation

Launch Napari and check that the widgets appear under the Plugins menu:

napari

You should see:

  • Welldata Widget
  • Gallery Widget
  • Training Widget
  • Aligned Plate Widget

Troubleshooting

Widgets not appearing in Plugins menu
Ensure the package is installed in the same environment as Napari. Run napari --info and check that omero-screen-napari is listed.
OMERO connection fails
Verify your .env file exists and contains valid credentials. Check that the OMERO server is reachable from your machine.
Import errors for zeroc-ice
The OMERO Python bindings require zeroc-ice. Platform-specific wheels are configured in the root pyproject.toml. If you encounter issues, check the omero-py documentation.