This code is intended to determine how open a stoma is from a stack of brightfield images.
Install the Python dependencies.
numpy==1.9.2 scipy==0.15.1 matplotlib==1.4.3 scikit-image==0.11.3 cv2==2.4.7 jicimagelib=0.3.1
Clone this repository.
git clone https://github.com/JIC-Image-Analysis/stomata-characterisation
Create a data directory structure.
cd stomata-characterisation mkdir -p data/raw
image.lif file the directory
python scripts/analyse_all_stomata.py data/raw/image.lif out
This produces the output directory
Inspect the images that show the stomata opening analysis performed.
Note that the algorithm does not find the correct minima for
Re-run the analysis for this stomate and time point with a higher Gaussian sigma smoothing for the average profile line.
python scripts/calculate_opening.py data/raw/image.lif 7 0 -s 2
Note that the stomate identifier is zero-indexed in the command above, i.e. 7 represents stomate 8.
Update the opening value for stomate 8 time point zero in the csv file
Configurations such as the stomate center, scale factor, z-slices to be
included, etc, are located in the global variable
util.STOMATA in the file