CellView

A DuckDB single-cell database for OMERO-Screen measurements.

AI / Agents

Skills
llms.txt
llms-full.txt

Developers

CellView Team

Meta

Requires: Python >=3.12,<3.15
Provides-Extra: test, explore
Package Info

A DuckDB-backed database for OMERO Screen CSV data with flexible import workflows

Status

Version: version

Python

License

Features

  • Import single-cell measurement data from OMERO Screen CSV exports
  • Flexible OMERO import with interactive project/experiment selection
  • DuckDB-powered efficient local storage and querying
  • Support for standalone plates and screen-based plates
  • Rich table-based user interfaces for data management
  • Export capabilities for downstream analysis

Installation

# Clone the repository
git clone https://github.com/HocheggerLab/omero-screen.git
# Change into the project directory
cd omero-screen/packages/cellview
# Create and activate virtual environment
uv venv
source .venv/bin/activate
# Install the package
uv pip install -e .

Usage

# Import from CSV file
cellview --csv /path/to/data.csv

# Import from OMERO plate (interactive mode)
cellview --plate-id 12345

# Display available projects
cellview --projects

# Export plate data
cellview --export-plate 67890

Project Structure

cellview/
 src/
    cellview/
        importers/     # Data import functionality
        exporters/     # Data export functionality
        db/           # Database operations
        utils/        # Utilities and state management
 tests/
 examples/

Enhanced OMERO Import

CellView now supports flexible OMERO plate imports that handle: - Standalone plates (not part of a screen) - Screen-based plates with tag-based project detection - Interactive confirmation with rich table displays - Project/experiment selection from existing options

Versioning

This project uses Semantic Versioning and Conventional Commits.

To bump the version use commitizen: https://commitizen-tools.github.io/commitizen/

cz bump

Contributing

  1. Fork the repository
  2. Create your feature branch (git checkout -b feature/amazing-feature)
  3. Commit your changes (cz commit)
  4. Push to the branch (git push origin feature/amazing-feature)
  5. Open a Pull Request

Authors

Created by Helfrid Hochegger Email: hh65@sussex.ac.uk

Dependencies

Requires Python 3.12 or greater

License

This project is licensed under the MIT License - see the LICENSE file for details

Acknowledgments

  • Built on DuckDB for efficient local data storage
  • Integrates with OMERO for high-content imaging data
  • Uses Rich for enhanced command-line interfaces