Pollen tube analysis
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scripts
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LICENSE.md
README.md
methodology.md
requirements.txt
runcontainer.sh

README.md

README

Scripts to identify pollen grains and tubes in images.

For information about the algorithms see the methodology.

Running the code

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.