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PlantCV

Plant phenotyping using computer vision.
https://github.com/danforthcenter/plantcv

bioinformatics image-analysis plant-phenotyping plantcv science

Last synced: 20 minutes ago
JSON representation

Repository metadata

Plant phenotyping with image analysis

Host: GitHub
URL: https://github.com/danforthcenter/plantcv
Owner: danforthcenter
License: mpl-2.0
Created: 2014-03-14T18:24:23.000Z (about 10 years ago)
Default Branch: main
Last Pushed: 2024-04-21T20:14:37.000Z (21 days ago)
Last Synced: 2024-04-22T12:06:58.276Z (20 days ago)
Topics: bioinformatics, image-analysis, plant-phenotyping, plantcv, science
Language: Python
Homepage:
Size: 467 MB
Stars: 612
Watchers: 45
Forks: 256
Open Issues: 74
Metadata Files:
- Readme: README.md
- Contributing: docs/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: docs/CODE_OF_CONDUCT.md

README

        ![builds](https://github.com/danforthcenter/plantcv/workflows/builds/badge.svg)

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[![Documentation Status](https://readthedocs.org/projects/plantcv/badge/?version=stable)](https://plantcv.readthedocs.io/en/stable/?badge=stable)

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/danforthcenter/plantcv-binder.git/master?filepath=index.ipynb)

[![Docker Pulls](https://img.shields.io/docker/pulls/danforthcenter/plantcv.svg)](https://hub.docker.com/r/danforthcenter/plantcv/)

[![GitHub release](https://img.shields.io/github/release/danforthcenter/plantcv.svg)](https://github.com/danforthcenter/plantcv/releases)

[![PyPI version](https://badge.fury.io/py/plantcv.svg)](https://badge.fury.io/py/plantcv)

![Conda](https://img.shields.io/conda/v/conda-forge/plantcv)

[![license](https://img.shields.io/github/license/danforthcenter/plantcv.svg)](https://github.com/danforthcenter/plantcv/blob/main/LICENSE)

[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](docs/CODE_OF_CONDUCT.md)

[![All Contributors](https://img.shields.io/badge/all_contributors-54-orange.svg?style=flat-square)](#contributors-)

# PlantCV: Plant phenotyping using computer vision

Please use, cite, and [contribute to](http://plantcv.readthedocs.io/en/latest/CONTRIBUTING/) PlantCV!

If you have questions, please submit them via the

[GitHub issues page](https://github.com/danforthcenter/plantcv/issues).

Follow us on twitter [@plantcv](https://twitter.com/plantcv).

***

## Introduction to PlantCV

PlantCV is an open-source image analysis software package targeted for plant phenotyping. PlantCV provides a common

programming and documentation interface to a collection of image analysis techniques that are integrated from a variety

of source packages and algorithms. PlantCV utilizes a modular architecture that enables flexibility in the design of

analysis workflows and rapid assimilation and integration of new methods. For more information about the project,

links to recorded presentations, and publications using PlantCV, please visit our homepage: 

.

### Quick Links

* [Documentation](http://plantcv.readthedocs.io/)

* [Interactive Documentation](https://mybinder.org/v2/gh/danforthcenter/plantcv-binder.git/master?filepath=index.ipynb)

* [Installation Instructions](https://plantcv.readthedocs.io/en/stable/installation/)

* [Updating/Changelog](https://plantcv.readthedocs.io/en/stable/updating/)

* [Public Image Datasets](http://plantcv.danforthcenter.org/pages/data.html)

* [Contribution Guide](https://plantcv.readthedocs.io/en/stable/CONTRIBUTING/)

* [Code of Conduct](https://plantcv.readthedocs.io/en/stable/CODE_OF_CONDUCT/)

* Downloads

  * [GitHub](https://github.com/danforthcenter/plantcv)

  * [PyPI](https://pypi.org/project/plantcv/)

  * [Conda-forge](https://anaconda.org/conda-forge/plantcv)

  * [Docker](https://hub.docker.com/r/danforthcenter/plantcv)

  * [Zenodo](https://doi.org/10.5281/zenodo.595522)

### Citing PlantCV

If you use PlantCV, please cite the [PlantCV publications](https://plantcv.danforthcenter.org/#plantcv-publications)

relevant to your work. To see how others have used PlantCV in their research, check out our list of 

[publications using PlantCV](https://plantcv.danforthcenter.org/#publications-using-plantcv).

***

## Issues with PlantCV

Please file any PlantCV suggestions/issues/bugs via our 

[GitHub issues page](https://github.com/danforthcenter/plantcv/issues). Please check to see if any related 

issues have already been filed.

***

## Contributors

  

    

      
_AFis-245
💻

      
_{Adam Dimech}
💻 📖 ⚠️ 🤔

      
_{Alexander Kutschera}
💻 📖 ⚠️

      
_{Alexandria Pokorny}
💻 📖 ⚠️

      
_{Andy Lin}
💻

      
_{Cesar Lizarraga}
💻 📖 ⚠️

      
_{Collin Luebbert}
💻

    

    

      
_{David Peery}
💻 📖 ⚠️ 🤔

      
_{Dhiraj Srivastava}
💻 📖 ⚠️

      
_{Dominik Schneider}
💻 📖 ⚠️ 🤔

      
_{Dr. Alexander Kutschera}
💻 🐛 💬

      
_{Eric Platon}
💻 📖 ⚠️

      
_{Fabian Dubois}
💻

      
_{Fabio Barbero}
💻

    

    

      
_{Garrot Yoan}
📖

      
_GrantKonkel
💻 📖

      
_{Haley Schuhl}
💻 📖 🚧 ✅ ⚠️ 📢 🤔 💬

      
_{Hudanyun Sheng}
💻 📖 ⚠️ 🤔

      
_Jake
💻 📖

      
_{Jeffrey Berry}
💻 📖 ⚠️ 🤔

      
_JoeDuenwald
📖

    

    

      
_{Jorge Gutierrez}
💻 📖 ⚠️ 📢 🤔 💬

      
_{Josh Sumner}
💻 📖 ⚠️ ✅ 🤔

      
_{Katie Murphy}
📖 ✅ 📢 🤔 📣

      
_KeelyBrown
💻

      
_{Malia Gehan}
📆 💻 📖 🔍 🧑‍🏫 📢 ✅ 🤔 💬 ⚠️

      
_Malinda
💻

      
_{Mark Wilson}
💻 📖 ⚠️

    

    

      
_Max
💻 📖 🤔

      
_{Noah Fahlgren}
📆 💻 📖 ⚠️ 🔍 🧑‍🏫 📢 ✅ 🤔 💬

      
_Sanazjd
💻 📖 ⚠️ 🤔

      
_SethPolydore
💻 📖 ⚠️

      
_{Steen Hoyer}
💻 📖 🤔

      
_{Stephan Summerer}
💻

      
_{Steven Wu}
💻

    

    

      
_{Stylopidae1793}
📖

      
_{TJ Schultz}
💻 🐛

      
_{adrianethompson}
💻 📖 ✅

      
_annacasto
💻 📖 ⚠️ ✅ 📢 🤔

      
_bganglia
💻 📖 ⚠️

      
_jgerardhodge
💻 📖 ⚠️

      
_jmgordon1223
📖

    

    

      
_jwheeler5
💻 📖 ⚠️

      
_kbgilbert
🎨

      
_lacostag
📖

      
_lchavez037
📖

      
_leowlima
📖

      
_mtwatso2-eng
💻

      
_natejly
💻

    

    

      
_scallen81
💻

      
_sdkenney42
📖

      
_typelogic
💻

      
_wurDevTim
💻 📖 ⚠️

      
_zeeuqsze
📖 ✅ 📢 🧑‍🏫

Owner metadata

Name: Donald Danforth Plant Science Center
Login: danforthcenter
Email:
Kind: organization
Description: Our Mission: Improve the Human Condition Through Plant Science
Website: https://danforthcenter.org
Location: St. Louis, MO
Twitter:
Company:
Icon url: https://avatars.githubusercontent.com/u/9678079?v=4
Repositories: 97
Last ynced at: 2024-04-16T01:03:45.399Z
Profile URL: https://github.com/danforthcenter

GitHub Events

Total

Fork event: 296
Create event: 821
Commit comment event: 5
Release event: 47
Issues event: 959
Watch event: 626
Delete event: 745
Member event: 16
Issue comment event: 2966
Push event: 3945
Pull request review event: 650
Pull request review comment event: 428
Pull request event: 1606

Last Year

Create event: 354
Delete event: 338
Fork event: 20
Issue comment event: 601
Issues event: 145
Member event: 4
Pull request event: 671
Pull request review comment event: 31
Pull request review event: 302
Push event: 1229
Release event: 4
Watch event: 96

Committers metadata

Last synced: about 3 hours ago

Total Commits: 6,122
Total Committers: 68
Avg Commits per committer: 90.029
Development Distribution Score (DDS): 0.655

Commits in past year: 1,258
Committers in past year: 23
Avg Commits per committer in past year: 54.696
Development Distribution Score (DDS) in past year: 0.641

Name	Email	Commits
Noah Fahlgren	n**n@g**m	2114
HaleySchuhl	h**l@g**m	1905
Hudanyun Sheng	h**g@g**m	421
maliagehan	m**g@g**m	375
JorgeGtz	j**r@g**m	276
Dominik Schneider	d**r@w**u	188
allcontributors[bot]	4****]	114
KeelyBrown	1****3	86
Dominik Schneider	d****h	78
David Peery	6****y	49
bganglia	b**2@g**m	45
JoeDuenwald	1****d	44
Bhatt	1****e	39
GrantKonkel	7****l	28
Max Feldman	m**n@g**m	25
Josh Sumner	5****r	24
annacasto	6****o	21
J. Steen Hoyer	j**r@w**u	20
deepsource-autofix[bot]	6****]	14
leowlima	l**a@d**g	13
sdkenney42	1****2	12
Daalen	t**n@w**l	12
jberry	j**7@y**m	12
calizarr	c**r@g**m	12
afinit	m**1@g**m	11
Duenwald	j**d@d**g	10
Stylopidae1793	1****3	10
aapokor	a****r	10
scallen81	s**n@d**g	10
Adam Dimech	a**h@a**u	9
and 38 more...

Committer domains:

Issue and Pull Request metadata

Last synced: 1 day ago

Total issues: 551
Total pull requests: 913
Average time to close issues: 4 months
Average time to close pull requests: 23 days
Total issue authors: 155
Total pull request authors: 58
Average comments per issue: 3.4
Average comments per pull request: 1.51
Merged pull request: 804
Bot issues: 0
Bot pull requests: 79

Past year issues: 99
Past year pull requests: 275
Past year average time to close issues: about 1 month
Past year average time to close pull requests: 5 days
Past year issue authors: 35
Past year pull request authors: 20
Past year average comments per issue: 2.46
Past year average comments per pull request: 1.11
Past year merged pull request: 232
Past year bot issues: 0
Past year bot pull requests: 66

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/danforthcenter/plantcv

Top Issue Authors

nfahlgren (111)
HaleySchuhl (81)
maliagehan (51)
dschneiderch (42)
AdamDimech (18)
MjBordalo (10)
EdwinP503 (6)
jshoyer (6)
AntonSax (6)
kmurphy61 (5)
RavinduDharmasena (5)
jdavidpeery (5)
calizarr (4)
k034b363 (4)
Mahi-Mai (4)

Top Pull Request Authors

nfahlgren (237)
HaleySchuhl (189)
allcontributors[bot] (66)
JoeDuenwald (54)
dschneiderch (43)
DannieSheng (31)
JorgeGtz (29)
maliagehan (25)
zeeuqsze (21)
k034b363 (14)
deepsource-autofix[bot] (13)
leowlima (13)
afinit (12)
sdkenney42 (12)
natejly (11)

Top Issue Labels

new feature (109)
help wanted (108)
enhancement (73)
bug (70)
documentation (39)
Epic (21)
update (12)
bugfix (8)
testing (7)
work in progress (5)
cleanup (5)
morphology-subpackage (3)
contributor (2)

Top Pull Request Labels

ready to review (303)
documentation (144)
enhancement (142)
new feature (119)
update (114)
bugfix (93)
contributor (56)
cleanup (49)
work in progress (41)
testing (18)
Objects class implementation (15)
bug (9)
morphology-subpackage (2)
Epic (1)
help wanted (1)

Package metadata

Total packages: 3
Total downloads:
- pypi: 2,775 last-month
Total docker downloads: 162
Total dependent packages: 0 (may contain duplicates)
Total dependent repositories: 25 (may contain duplicates)
Total versions: 77
Total maintainers: 1

pypi.org: plantcv

An image processing package for plant phenotyping.

Homepage: http://plantcv.danforthcenter.org
Documentation: https://plantcv.readthedocs.io/
Licenses: MIT
Latest release: 4.2.1 (published 4 months ago)
Last Synced: 2024-05-11T09:35:23.519Z (1 day ago)
Versions: 33
Dependent Packages: 0
Dependent Repositories: 25
Downloads: 2,775 Last month
Docker Downloads: 162
Rankings:
- Dependent repos count: 2.899%
- Docker downloads count: 4.316%
- Average: 5.814%
- Downloads: 5.935%
- Dependent packages count: 10.108%
Maintainers (1)
- danforthcenter

proxy.golang.org: github.com/danforthcenter/plantcv

Homepage:
Documentation: https://pkg.go.dev/github.com/danforthcenter/plantcv#section-documentation
Licenses: mpl-2.0
Latest release: v4.2.1+incompatible (published 4 months ago)
Last Synced: 2024-05-11T09:35:23.443Z (1 day ago)
Versions: 32
Dependent Packages: 0
Dependent Repositories: 0
Rankings:
- Dependent packages count: 9.049%
- Average: 9.627%
- Dependent repos count: 10.204%

conda-forge.org: plantcv

Homepage: https://plantcv.org
Licenses: MPL-2.0
Latest release: 3.14.1 (published almost 2 years ago)
Last Synced: 2024-05-11T09:35:26.415Z (1 day ago)
Versions: 12
Dependent Packages: 0
Dependent Repositories: 0
Rankings:
- Dependent repos count: 34.025%
- Average: 42.6%
- Dependent packages count: 51.175%

Dependencies

Dockerfile docker

jupyter/minimal-notebook latest build

.github/workflows/publish-package.yml actions

actions/checkout main composite
actions/setup-python main composite

.github/workflows/continuous-integration.yml actions

actions/checkout main composite
actions/setup-python main composite
codecov/codecov-action v1 composite

docs/requirements.txt pypi

mkdocs >1

environment.yml pypi

requirements.txt pypi

altair *
dask *
dask-jobqueue *
matplotlib >=1.5
numpy >=1.11
opencv-python *
pandas *
python-dateutil *
scikit-image >=0.19
scikit-learn *
scipy *
statsmodels *
vl-convert-python *
xarray >=2022.11.0

setup.py pypi

Score: 18.74535485559987