README.md
In edwardpmorris/FAST_LeafArea: Use ImageJ to derive leaf surface area from scanned images
FAST_LeafArea
A collection of scripts for processing images of plant structures collected using a simple flatbed scanner. These are just control scripts for automated processing using the R package LeafArea (https://cran.r-project.org/web/packages/LeafArea/index.html), which controls ImageJ.
Status
Under development and specific to the FAST plant scan images.
Resources
Inspiration
Imagej macros for defining leaf area
Roadmap
- adjust run.ij to accomodate ImageJ2 (fiji)
- Dockerise Java and ImageJ, see fiji Dockerfiles.
- Adjust LeafArea::run.ij so as to call Docker container for image processing, see 'running headless' in example.
- R package for controlling Docker containers
- check if image stacking option is more efficient
Image processing workflow
edwardpmorris/FAST_LeafArea documentation built on May 15, 2019, 11:03 p.m.
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
FAST_LeafArea
A collection of scripts for processing images of plant structures collected using a simple flatbed scanner. These are just control scripts for automated processing using the R package LeafArea (https://cran.r-project.org/web/packages/LeafArea/index.html), which controls ImageJ.
Status
Under development and specific to the FAST plant scan images.
Resources
Inspiration
Imagej macros for defining leaf area
Roadmap
- adjust run.ij to accomodate ImageJ2 (fiji)
- Dockerise Java and ImageJ, see fiji Dockerfiles.
- Adjust LeafArea::run.ij so as to call Docker container for image processing, see 'running headless' in example.
- R package for controlling Docker containers
- check if image stacking option is more efficient
Image processing workflow
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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