Single cell Morphology Quality Control

🌠 Navigate the cosmos of single-cell morphology with confidence — coSMicQC keeps your data on course!

Contents

• Single cell Morphology Quality Control
  • Contents
  • Overview
  • Repo Contents
  • System Requirements
  • Installation Guide
    • Stable release (PyPI)
    • Development version (from source)
  • Demo
  • Results
  • License
  • Issues
  • Citation

Overview

coSMicQC is a Python package to evaluate converted single-cell morphology outputs from CytoTable. Technical artifacts can arise during segmentation, leading to issues such as under-segmentation, over-segmentation, or the erroneous segmentation of background noise, smudges, or bright artifacts. By utilizing specific morphological features extracted with CellProfiler, you can identify technically incorrect segmentations and label or remove them before downstream analysis.

Please confer with our docsite for more comprehensive information about the project: https://cytomining.github.io/coSMicQC/main/

🌟 Check out our blog post for a deeper background and how coSMicQC can help.

Repo Contents

• src/cosmicqc: coSMicQC source code.
• tests: test suite.
• docs: documentation sources and examples.
• media: project assets (e.g., coverage badge).
• reports: generated artifacts (figures, notebooks, or summaries).

System Requirements

• Python: >=3.10 (tested through 3.13).
• RAM/CPU: standard laptop/desktop is sufficient for typical plate-sized datasets; larger screens benefit from more RAM/cores for faster QC/plotting.
• OS: Linux, macOS, and Windows are supported via Python; CI tests run on GitHub Actions.

Installation Guide

Stable release (PyPI)

pip install coSMicQC

Development version (from source)

pip install git+https://github.com/cytomining/coSMicQC.git
# or with poetry for local development
poetry install --with dev

Demo

• Examples and notebooks live under docs/src/examples and the published docs: https://cytomining.github.io/coSMicQC
• Quickstart blog post: https://waysciencelab.com/2024/12/20/cosmicqc.html

Results

• Test and lint status:
• Coverage:

License

BSD-3-Clause; see LICENSE.

Issues

Please open issues or feature requests at https://github.com/cytomining/coSMicQC/issues.

Citation

If you use coSMicQC in your work, please cite:

• Software DOI: 10.5281/zenodo.14888111
• Preprint: 10.1101/2025.10.14.682427
• Citation metadata: CITATION.cff