Single cell Morphology Quality Control
🌠 Navigate the cosmos of single-cell morphology with confidence — coSMicQC keeps your data on course!
coSMicQC is a Python package to evaluate converted single-cell morphology outputs from CytoTable.
It can be challenging to get "perfect" single-cell compartment segmentation across large high-throughput screens when performing object detection in CellProfiler (or similar software). 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.
In single-cell analysis, intriguing phenotypes often emerge by examining morphological differences. However, technical outliers in the data can obscure these biological insights, compromising the validity of the findings.
By utilizing specific morphological features extracted with CellProfiler, particularly AreaShape features, you can identify technically incorrect segmentations. These can then be labeled or removed before further preprocessing steps, such as those performed with pycytominer.
🌟 Check out our blog post on this for a greater understanding of the background and how coSMicQC can help you!
Installation
Install coSMicQC from PyPI or from source:
# install from pypi
pip install coSMicQC
# install directly from source
pip install git+https://github.com/cytomining/coSMicQC.git
Contributing, Development, and Testing
Please see our contributing documentation for more details on contributions, development, and testing.
References
2 maintainers
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file cosmicqc-0.0.0.tar.gz.
File metadata
- Download URL: cosmicqc-0.0.0.tar.gz
- Upload date:
- Size: 16.3 kB
- Tags: Source
- Uploaded using Trusted Publishing? Yes
- Uploaded via: twine/6.1.0 CPython/3.13.7
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
ce4bc387b52b13c199405a3bc36df9e79af04d3f963c0930fd906dde1f1ad5a1
|
|
| MD5 |
5b9e53d06197db3cb9154e066f4473b9
|
|
| BLAKE2b-256 |
69f4c77d5f9e98de59a9ab6b737fe72ceb5cd8f4e50950a80b0207a583bb9c2a
|
Provenance
The following attestation bundles were made for cosmicqc-0.0.0.tar.gz:
Publisher:
publish-pypi.yml on cytomining/coSMicQC
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
cosmicqc-0.0.0.tar.gz -
Subject digest:
ce4bc387b52b13c199405a3bc36df9e79af04d3f963c0930fd906dde1f1ad5a1 - Sigstore transparency entry: 606358920
- Sigstore integration time:
-
Permalink:
cytomining/coSMicQC@d152e9fa1752744d7c5497c5228ec6efdb8ce6c3 -
Branch / Tag:
refs/tags/v1.0.0 - Owner: https://github.com/cytomining
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish-pypi.yml@d152e9fa1752744d7c5497c5228ec6efdb8ce6c3 -
Trigger Event:
release
-
Statement type:
File details
Details for the file cosmicqc-0.0.0-py3-none-any.whl.
File metadata
- Download URL: cosmicqc-0.0.0-py3-none-any.whl
- Upload date:
- Size: 15.6 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? Yes
- Uploaded via: twine/6.1.0 CPython/3.13.7
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
773f092559a0dd5aff010c5ef00b416b129482c937d10d8f5328b7cecf76606c
|
|
| MD5 |
56e776a8dbf7cdf37ce63c7c8ca3af67
|
|
| BLAKE2b-256 |
2ebd98ad535d84153bf7843b402dcc470a7d038040405488b19bc1b4f666db8c
|
Provenance
The following attestation bundles were made for cosmicqc-0.0.0-py3-none-any.whl:
Publisher:
publish-pypi.yml on cytomining/coSMicQC
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
cosmicqc-0.0.0-py3-none-any.whl -
Subject digest:
773f092559a0dd5aff010c5ef00b416b129482c937d10d8f5328b7cecf76606c - Sigstore transparency entry: 606358924
- Sigstore integration time:
-
Permalink:
cytomining/coSMicQC@d152e9fa1752744d7c5497c5228ec6efdb8ce6c3 -
Branch / Tag:
refs/tags/v1.0.0 - Owner: https://github.com/cytomining
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish-pypi.yml@d152e9fa1752744d7c5497c5228ec6efdb8ce6c3 -
Trigger Event:
release
-
Statement type:
