BluVision Macro - a software for automated powdery mildew and rust disease quantification on detached leaves.
BluVision Macro - a software for automated powdery mildew and rust disease quantification on detached leaves. - Published in JOSS (2020)
Science Score: 93.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README and JOSS metadata -
○Academic publication links
-
○Committers with academic emails
-
○Institutional organization owner
-
✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Repository
Macrobot is an open source image analysis software for studying plant-pathogen interactions on macroscopic level.
Basic Info
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 9
- Releases: 3
Topics
Metadata Files
README.md
About macrobot software
Macrobot is an image analysis software for studying plant-pathogen interactions on macroscopic level. Currently the macrobot software can detect and quantify the following plant-pathogen interactions: - Barley powdery mildew (Blumeria graminis f. sp hordei) - Wheat powdery mildew (Blumeria graminis f. sp tritici) - Wheat yellow (stripe) rust (Puccinia striiformis f.sp. tritici) - Wheat brown (leaf) rust (P. graminis f. sp. tritici)
Figure 1: Powdery mildew on barley plants
The hardware system is based on a custom fully automated multispectral 2D imaging station (Figure 2).
Figure 2: Macrobot Module
See the macrobot hardware in action: https://www.youtube.com/watch?v=SmoKQ_uMp34&t=56s
The entire pipline from image aquisition to image analysis is shown in Figure 3.
Figure 3: Software pipeline
Citation
Lueck et al., (2020). BluVision Macro - a software for automated powdery mildew and rust disease quantification on detached leaves.. Journal of Open Source Software, 5(51), 2259, https://doi.org/10.21105/joss.02259
Documentation
https://macrobot.readthedocs.io/en/latest/index.html
Installation
Macrobot software was build and successfully tested on Windows operating system (Windows 7 and 10).
Option 1: Anaconda
Download and install Anaconda: (https://www.anaconda.com/distribution/)
Option 2: Miniforge
[!IMPORTANT] Note: Due to Anaconda's licensing limitations (maximum of 200 users per organization), we recommend considering an alternative, Miniforge, especially for larger teams or open-source projects.
Miniforge is a lightweight, community-driven alternative to Anaconda. It provides similar functionality and is free from licensing restrictions.
Download Miniforge 3 for Windows operating system: https://github.com/conda-forge/miniforge/releases/download/24.9.2-0/Miniforge3-Windows-x86_64.exe
Choose the installer appropriate for your operating system and follow the installation instructions provided on the download page.
Install macrobot software
conda create --name macrobot_env python=3.7
conda activate macrobot_env
conda install pip
pip install macrobot
Usage
- Create a folder for the result. We will create a new folder on the desktop called mb_results.
- Open the Ananconda prompt and activate your macrobot environment if you are not already there.
conda activate macrobot - Macrobot is a command line program which requires the following arguments:
- source path (-s) - the path with the images coming from the Macrobot hardware system
- destination path (-d) - the path to store the results
- pathogen (-p) - which pathogen to predict ("mildew", "bipolaris" or "rust")
- For a test case we will use a test image set which will be automatically downloaded by the start of the software. To tell the software to use the test images, we will enter "test_images" for the source path -s argument
- Start the software with the following command for mildew (adapt the destination path):
Mildew: mb -s test_images -d C:\Users\name\Desktop\mb_results\ -p mildew
Rust:
mb -s test_images -d C:\Users\name\Desktop\mb_results\ -p rust
Bipolaris:
mb -s test_images -d C:\Users\name\Desktop\mb_results\ -p bipolaris
6. In your destination folder should appear all results:
* A csv file with the predicted values per leaf
* A report html file in folder report which allows and easy control over the pipeline.
* Images created by the software (white=pathogen, red=leaf detection, black=background)
If you want to use a real world experiments, make sure to provide the following folder structure with five images per plate (see documentation)
Tests
cd to installation path and test folder e.g. d:\Anaconda\envs\mb_test\Lib\site-packages\macrobot\tests
Run pytest:
pytest
Contributions:
We are strongly looking for contributions, some ideas how to support our software could be found here: https://github.com/snowformatics/macrobot/wiki/Contributions
References:
https://github.com/snowformatics/macrobot/wiki/References
Owner
- Name: snowformatics
- Login: snowformatics
- Kind: user
- Website: https://snowformatics.github.io/
- Twitter: snowformatics
- Repositories: 21
- Profile: https://github.com/snowformatics
https://www.buymeacoffee.com/snowforamtics
JOSS Publication
BluVision Macro - a software for automated powdery mildew and rust disease quantification on detached leaves.
Authors
Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung Gatersleben, Stadt Seeland, Sachsen-Anhalt
Julius Kühn-Institut Quedlinburg, Sachsen-Anhalt
Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung Gatersleben, Stadt Seeland, Sachsen-Anhalt
Editor
Matthew Sottile
Tags
plant phenotyping powdery mildew barley wheat rust pucchinia python pathogenGitHub Events
Total
- Push event: 19
Last Year
- Push event: 19
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| snowformatics | l****s@g****m | 114 |
| luecks@gmail.com | S****2 | 112 |
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 15
- Total pull requests: 0
- Average time to close issues: about 1 month
- Average time to close pull requests: N/A
- Total issue authors: 6
- Total pull request authors: 0
- Average comments per issue: 1.13
- Average comments per pull request: 0
- Merged pull requests: 0
- 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
- snowformatics (8)
- phckopper (3)
- AoifeHughes (1)
- mjsottile (1)
- Douchkov (1)
- jizecn (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- jinja2 *
- numpy *
- opencv-python *
- pytest *
- scikit-image *
- sphinx-autoapi *
- jinja2 *
- numpy *
- opencv-python *
- pytest *
- scikit-image *
- sphinx-autoapi *
- MarkupSafe 2.0.1
- jinja2 2.10.3
- numpy 1.18.3
- opencv-python 4.2.0.34
- pytest 5.4.1
- python 3.7
- scikit-image 0.16.2