edwardpmorris / 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).

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

• Easy-Leaf-Area

Imagej macros for defining leaf area

• leafarea

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