Science Score: 59.0%
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○CITATION.cff file
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✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
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✓Committers with academic emails
1 of 4 committers (25.0%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (14.0%) to scientific vocabulary
Keywords
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Repository
Single cell Morphology Quality Control (coSMicQC)
Basic Info
- Host: GitHub
- Owner: cytomining
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Homepage: https://cytomining.github.io/coSMicQC/
- Size: 226 MB
Statistics
- Stars: 8
- Watchers: 2
- Forks: 3
- Open Issues: 19
- Releases: 15
Topics
Metadata Files
README.md
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:
```shell
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
Owner
- Name: cytomining
- Login: cytomining
- Kind: organization
- Repositories: 27
- Profile: https://github.com/cytomining
GitHub Events
Total
- Issues event: 6
- Watch event: 1
- Delete event: 8
- Issue comment event: 14
- Push event: 22
- Pull request review comment event: 21
- Pull request event: 30
- Pull request review event: 34
- Create event: 7
Last Year
- Issues event: 6
- Watch event: 1
- Delete event: 8
- Issue comment event: 14
- Push event: 22
- Pull request review comment event: 21
- Pull request event: 30
- Pull request review event: 34
- Create event: 7
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| dependabot[bot] | 4****] | 79 |
| Dave Bunten | d****n@c****u | 56 |
| Jenna Tomkinson | 1****n | 4 |
| Vincent Rubinetti | v****i@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 5
- Total pull requests: 103
- Average time to close issues: N/A
- Average time to close pull requests: 2 days
- Total issue authors: 3
- Total pull request authors: 3
- Average comments per issue: 0.0
- Average comments per pull request: 0.73
- Merged pull requests: 88
- Bot issues: 0
- Bot pull requests: 80
Past Year
- Issues: 5
- Pull requests: 103
- Average time to close issues: N/A
- Average time to close pull requests: 2 days
- Issue authors: 3
- Pull request authors: 3
- Average comments per issue: 0.0
- Average comments per pull request: 0.73
- Merged pull requests: 88
- Bot issues: 0
- Bot pull requests: 80
Top Authors
Issue Authors
- jenna-tomkinson (3)
- MikeLippincott (1)
Pull Request Authors
- dependabot[bot] (80)
- d33bs (21)
- jenna-tomkinson (2)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
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- tomli 2.0.1
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- pytest ^8.2.0 develop
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- python >=3.9,<3.13
- scipy ^1.13.0
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