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.
Under development and specific to the FAST plant scan images.
- 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
