Take an image of a petris dish with cultures and detect the culture circle. Based on that calculate the area and the growth differences on daily basis.
pip install virtualenv
pip install -r requirements.txt
VIA: VGG Image Annotator (VIA) can be downloaded from here.
Rename all pictures and put it into the same folder. Do this by running
python src/renaming.py
Then use VIA to circle all the colonies. An example of this looks like the picture below.
After all (!) pictures have been annotated, run dataWrangler.py to format the annotation.csv into a nice data frame for further use. needs an update
python src/dataWrangler.py
Run the notebook, which will create super nice interactive bokeh plots! See the data/growth_media.html as an example.