https://github.com/cellprofiler/cellprofiler-analyst
Open-source software for exploring and analyzing large, high-dimensional image-derived data.
Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.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
17 of 43 committers (39.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.7%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Open-source software for exploring and analyzing large, high-dimensional image-derived data.
Basic Info
- Host: GitHub
- Owner: CellProfiler
- License: other
- Language: Python
- Default Branch: master
- Homepage: http://cellprofileranalyst.org
- Size: 70.8 MB
Statistics
- Stars: 158
- Watchers: 20
- Forks: 75
- Open Issues: 71
- Releases: 7
Topics
Metadata Files
README.md
| Version | Documentation | Forum |
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CellProfiler Analyst allows interactive exploration and analysis of data, particularly from high-throughput, image-based experiments. Included is a supervised machine learning system which can be trained to recognize complex and subtle phenotypes, for automatic scoring of millions of cells.
Learn more about CellProfiler Analyst
This is the developer site for CellProfiler Analyst. The regular home page for CellProfiler Analyst is here: https://cellprofileranalyst.org/
Installation
Download CellProfiler Analyst
When running from source, CellProfiler Analyst requires JDK 1.8 to be installed (not just JRE). Check the Java path.
Please note that this is the development branch of CPA and it will be updated on regular basis.
Find all releases here.
For a head start, download example dataset here: Example Dataset for CPA (zipped)
Developer build
Building CPA on your machine requires CellProfiler dependencies. Check the wiki for more detailed installation instructions.
- Pandas
- Seaborn
- Scikit-learn
- Python-Javabridge
- Verlib
- Python-bioformats
Documentation
https://cellprofileranalyst.org/manuals
Wiki
https://github.com/CellProfiler/CellProfiler-Analyst/wiki
Forum
CellProfiler Analyst development is discussed on the CellProfiler Forum list.
https://forum.image.sc/tag/cellprofiler-analyst/
How to file new issues
Please attach sufficient information to reproduce the bug. For many bugs, it is appropriate to attach a properties file, a training set, or a screenshot.
How to cite
David Dao, Adam N Fraser, Jane Hung, Vebjorn Ljosa, Shantanu Singh and Anne E Carpenter
CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets
Bioinformatics (2016) doi:10.1093/bioinformatics/btw390
Thouis R Jones, In Han Kang, Douglas B Wheeler, Robert A Lindquist, Adam Papallo, David M Sabatini, Polina Golland and Anne E Carpenter
CellProfiler Analyst: data exploration and analysis software for complex image-based screens
BMC Bioinformatics (2008) doi:10.1186/1471-2105-9-482
Contributors
David Dao, Adam Fraser, David Stirling, Pearl Ryder, Beth Cimini, Vebjorn Ljosa, Thouis R. Jones, Jane Hung, Shantanu Singh, Mark Bray, Lee Kamentsky, Anne Carpenter
Kudos
David Logan, Allen Goodman, Alison Kozol, Mohammad Hossein Rohban
Copyright 2021, The Broad Institute of MIT and Harvard. Distributed under the BSD license.
Owner
- Name: CellProfiler
- Login: CellProfiler
- Kind: organization
- Location: Cambridge, MA
- Repositories: 30
- Profile: https://github.com/CellProfiler
Software for quantitative analysis of biological images
GitHub Events
Total
- Release event: 1
- Issues event: 6
- Watch event: 9
- Delete event: 2
- Issue comment event: 2
- Push event: 23
- Pull request event: 6
- Fork event: 3
Last Year
- Release event: 1
- Issues event: 6
- Watch event: 9
- Delete event: 2
- Issue comment event: 2
- Push event: 23
- Pull request event: 6
- Fork event: 3
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| afraser | a****r@1****7 | 1,123 |
| David Stirling | d****g@b****g | 280 |
| thouis | t****s@1****7 | 172 |
| David Dao | c****o@g****m | 118 |
| mbray | m****y@1****7 | 110 |
| Vebjorn Ljosa | v****n@l****m | 110 |
| ljosa | l****a@1****7 | 89 |
| jhung0 | j****g@b****g | 86 |
| shntnu | s****h@b****g | 46 |
| Mark Bray | m****y@b****g | 35 |
| imtiazKHAN | i****n@b****g | 30 |
| auguste | a****e@1****7 | 25 |
| Lee Kamentsky | l****k@b****g | 16 |
| Thouis (Ray) Jones | t****s@g****m | 12 |
| dlogan | d****n@1****7 | 10 |
| Rebecca Senft | s****t@g****u | 10 |
| leek | l****k@1****7 | 9 |
| pearlryder | p****r@b****g | 9 |
| ikhan | i****n@1****7 | 8 |
| shsingh | s****h@1****7 | 7 |
| David Logan | d****n@b****g | 7 |
| Shantanu Singh | s****h@p****g | 5 |
| panthony | p****y@1****7 | 5 |
| klmadden | k****n@1****7 | 5 |
| Auguste Genovesio | a****e@p****g | 4 |
| Egor Zindy | e****y@g****m | 3 |
| DavidStirling | d****0@h****k | 3 |
| Mario Emmenlauer | m****o@e****e | 3 |
| Beth Cimini | b****7 | 3 |
| Rebecca Senft | 2****1 | 3 |
| and 13 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: almost 2 years ago
All Time
- Total issues: 92
- Total pull requests: 8
- Average time to close issues: almost 2 years
- Average time to close pull requests: about 1 month
- Total issue authors: 9
- Total pull request authors: 4
- Average comments per issue: 2.83
- Average comments per pull request: 0.88
- Merged pull requests: 8
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- dlogan (26)
- braymp (24)
- ljosa (14)
- jhung0 (8)
- LeeKamentsky (7)
- daviddao (6)
- AnneCarpenter (4)
- thouis (1)
- dbsi-pinkman (1)
- sclamons (1)
- nm728 (1)
- emiglietta (1)
- Andaukmoan (1)
- DavidStirling (1)
Pull Request Authors
- daviddao (4)
- ttwimlex (2)
- gnodar01 (2)
- stulacy (1)
- radioxoma (1)
- bethac07 (1)
- shntnu (1)
- DavidStirling (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- Pillow *
- boto3 *
- botocore *
- imagecodecs *
- imageio *
- joblib *
- matplotlib *
- mock *
- mysqlclient *
- numpy *
- pandas *
- progressbar *
- python-bioformats *
- python-javabridge *
- pytz *
- requests *
- scikit-learn *
- scipy *
- seaborn *
- verlib *
- wxPython *
- Pillow >=8.1.0
- boto3 ==1.17.15
- botocore ==1.20.15
- imagecodecs >=2021.2.26
- imageio >=2.9.0
- joblib >=1.0.1
- matplotlib ==3.3.4
- mock >=4.0.3
- mysqlclient >=2.0.3
- numpy >=1.20.1
- pandas >=1.2.2
- progressbar >=2.5
- python-bioformats >=4.0.4
- python-javabridge >=4.0.3
- pytz >=2021.1
- requests >=2.25.1
- scikit-learn >=0.24.1
- scipy >=1.6.1
- seaborn >=0.11.1
- tifffile >=2021.3.31
- verlib ==0.1
- wxPython ==4.1.0
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/create-release v1 composite
- actions/download-artifact v1 composite
- actions/setup-java v1 composite
- actions/setup-python v2 composite
- actions/upload-artifact v1 composite
- actions/upload-artifact v2 composite
- actions/upload-release-asset v1 composite