Scripts to identify pollen grains and tubes in images.

For information about the algorithms see the methodology.

To run the code, first create the data and output directories:

mkdir {data,output}

Then copy the data to be analysed into the data directory. Then, start the docker container with:

bash runcontainer.sh

If the data has been collected using a Leica microscope run:

python /code/annotate.py /data/ /output/

If the data has been collected using a Nikon E800 microscope run:

python /code/nikonE800_annotate.py /data/ /output/

The analysis will be available in the output directory.