Download the source code from GitHub:

https://github.com/JIC-Image-Analysis/leaf-cell-polarisation-tensors

This image analysis project has been setup to take advantage of a technology known as Docker.

This means that you will need to:

1. Download and install the Docker Toolbox
2. Build the local docker image:

$ cd docker
$ bash build_docker_images.sh
$ cd ../

1. Put your image file, e.g. genotype1.tif into the data directory.
2. Start a docker session in the analysis container

$ bash run_analysis_container.sh
[root@25278c5a93ec /]#

3. Run the automated analysis script on the image

[root@25278c5a93ec /]# python /scripts/automated_analysis.py /data/genotype1.tif /output/genotype1

1. Start a docker session in the webapp continer

$ bash run_webapp_container.sh
[root@125b9dd8d3df /]#

2. Start the webapp

[root@125b9dd8d3df /]# python /scripts/webapp.py /output/genotype1/

3. Point a web browser at http://192.168.99.100/ and start editing