πŸ“‹ Documentation Version Notice

You're reading the documentation for a development version (master). For the latest released version, please have a look at v1.7.

Developer Getting Started

Tip

πŸŽ₯ BIOMERO Videos: Start with the conceptual introduction or explore the short technical architecture clips.

Quick Setup for Development

Clone the repository and set up your development environment:

git clone --recurse-submodules https://github.com/Cellular-Imaging-Amsterdam-UMC/NL-BIOMERO.git
cd NL-BIOMERO

# Setup environment
# Edit .env with your configuration if needed

# Start development containers (web server will NOT be running yet)
docker-compose -f docker-compose-dev.yml up -d --build

# Clone OMERO.biomero plugin for development
cd ..  # Go to parent directory (both repos must be in same parent folder)
git clone https://github.com/NL-BioImaging/OMERO.biomero.git
cd OMERO.biomero

# Build the frontend (required before starting web server)
cd webapp
# On Windows:
corepack yarn install
corepack yarn build
# On Linux:
# yarn install
# yarn build
cd ..

# Start OMERO web server (use WSL on Windows)
./omero-init.sh

# OMERO web is now available at localhost:4080

Development Features

The development compose file includes:

  • Containers that don’t exit when web server stops (for easier development)

  • Development-specific configurations

  • Special container setup for easier debugging

  • Integration with local OMERO.biomero development

Note

Important: The -dev compose file starts containers but not the web server. The web server is controlled by OMERO.biomero’s ./omero-init.sh script.

Note

Frontend Build Required: Before running ./omero-init.sh, you must build the OMERO.biomero frontend assets. On Windows, you may need to install corepack and yarn first.

Note

For detailed OMERO.biomero setup (including Node.js/yarn installation) and development workflow, see the OMERO.biomero Setup and Development Guide.

Architecture Overview

NL-BIOMERO architecture overview

BIOMERO 2.0 architecture showing the integration of containerized analysis workflows (BIOMERO 1.0), preprocessing workflows (BIOMERO 2.0), and the unified OMERO.biomero web interface with OMERO.forms for metadata collection.

See Architecture Overview for the component boundaries, import and analysis pipelines, monitoring, and workflow-development model.

Deployment Documentation