Single cell Morphology Quality Control

PyPI - Version Coverage Status

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

Single cell Morphology Quality Control

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 uv for local development
uv sync

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

Release files for cosmicqc 1.1.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for cosmicqc 1.1.2
File	Size	Uploaded
cosmicqc-1.1.2.tar.gz	375.6 kB	Sep 3, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for cosmicqc 1.1.2
File	Interpreter	ABI	Platform	Reset
cosmicqc-1.1.2-py3-none-any.whl 19.7 kB Sep 3, 2026	Python 3	none	any	Details

Total release size: 395.3 kB

Release files / cosmicqc-1.1.2.tar.gz

Download URL	cosmicqc-1.1.2.tar.gz
Size	375.6 kB
Tags	Source
SHA-256 checksum How to use checksums	`86dde2c85e1380d6f72ea79a127e47d3c343c9e6e51e7c417676334cdc228cd2`
BLAKE2b-256 checksum How to use checksums	`ac429d2e36d644bf95625841ec4c7d31612223855c5b4e26cc73fd4856ebb5c9`
Upload date	Sep 3, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/cytomining/coSMicQC
Publishing commit: github.com/cytomining/coSMicQC/tree/f5b9c2a551d81f38733545b2318330316615c141

Workflow

Publishing configuration: github.com/cytomining/coSMicQC/blob/f5b9c2a551d81f38733545b2318330316615c141/.github/workflows/publish-pypi.yml
Publishing logs: github.com/cytomining/coSMicQC/actions/runs/33807833547/attempts/1

Artifact

Subject: cosmicqc-1.1.2.tar.gz
SHA-256 checksum: 86dde2c85e1380d6f72ea79a127e47d3c343c9e6e51e7c417676334cdc228cd2 Verifying attestations

Release files / cosmicqc-1.1.2-py3-none-any.whl

Download URL	cosmicqc-1.1.2-py3-none-any.whl
Size	19.7 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`cbf84728d0b8eec9d03f5135f837e889f1a96d911c492f3b2b9a8bd2ffd2e04b`
BLAKE2b-256 checksum How to use checksums	`3ea0d29b86c15390bc4e361a992d38441b7dbf4a37808c11c78a5db3dc932a8d`
Upload date	Sep 3, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/cytomining/coSMicQC
Publishing commit: github.com/cytomining/coSMicQC/tree/f5b9c2a551d81f38733545b2318330316615c141

Workflow

Publishing configuration: github.com/cytomining/coSMicQC/blob/f5b9c2a551d81f38733545b2318330316615c141/.github/workflows/publish-pypi.yml
Publishing logs: github.com/cytomining/coSMicQC/actions/runs/33807833547/attempts/1

Artifact

Subject: cosmicqc-1.1.2-py3-none-any.whl
SHA-256 checksum: cbf84728d0b8eec9d03f5135f837e889f1a96d911c492f3b2b9a8bd2ffd2e04b Verifying attestations