Package to support reproducible image annotation workflows for AI training using OMERO data repositories. This Python package provides Jupyter widgets and tools for reproducible annotation, training, and inference using micro-SAM, Cellpose, and other AI models directly with OMERO datasets.
- Interactive Jupyter widgets for OMERO connection and workflow configuration
- AI-assisted annotation using micro-SAM integration
- Reproducible workflows with YAML configuration tracking
- Training data preparation for BiaPy and DL4MicEverywhere
- Direct OMERO integration with automatic result storage
# Recommended: Using pixi
pixi init myproject && cd myproject
pixi add micro_sam
pixi add --pypi omero-annotate-ai
pixi shell
# Alternative: Conda + pip
conda install -c conda-forge micro-sam
pip install omero-annotate-ai📖 See Installation Guide for detailed instructions and troubleshooting.
OMERO Connection Widget
Annotation Pipeline Widget
from omero_annotate_ai import create_omero_connection_widget, create_workflow_widget, create_pipeline
# Connect to OMERO
conn_widget = create_omero_connection_widget()
conn_widget.display()
conn = conn_widget.get_connection()
# Configure annotation workflow
workflow_widget = create_workflow_widget(connection=conn)
workflow_widget.display()
config = workflow_widget.get_config()
# Run annotation pipeline
pipeline = create_pipeline(config, conn)
table_id, processed_images = pipeline.run_full_workflow()Try these example notebooks to get started:
For batch processing and reproducible workflows, you can also use YAML configuration files:
from omero_annotate_ai.core.annotation_config import load_config
from omero_annotate_ai.core.annotation_pipeline import create_pipeline
# Load configuration from YAML
config = load_config("annotation_config.yaml")
conn = create_connection(host="omero.server.com", user="username")
# Run annotation pipeline
pipeline = create_pipeline(config, conn)
results = pipeline.run_full_workflow()See the YAML Configuration Guide for complete documentation.
- Installation Guide - Detailed installation instructions and troubleshooting
- micro-SAM Tutorial - Step-by-step annotation workflow tutorial
- YAML Configuration Guide - Complete YAML configuration reference and examples
- API Reference - Complete API documentation
- Examples - Jupyter notebook tutorials
We welcome contributions! For development setup:
- Fork the repository
- Clone and set up development environment:
git clone https://github.com/YOUR_USERNAME/omero_annotate_ai.git cd omero_annotate_ai pixi install - Make changes and run tests:
pixi run pytest - Submit a pull request
See Installation Guide - Development Setup for detailed instructions.
Maarten Paul - [email protected]
Acknowledgments: Developed within the NL-BioImaging infrastructure, funded by NWO.