By Zoë McGinnis
First, please install python3. You can find instructions to do so for your specific OS here.
If you are planning to use only the jupyter notebook version of the cell counter, run pip3 install jupyter notebook.
If you are planning to use the regular python version of the code, run the following command from your terminal to install the required libraries: pip3 install -r requirements.txt.
First, navigate to this folder, bsc, using the terminal. If it's in your home directory, you can just run cd bsc. Next, move the image you want to use into the folder called originals. Make sure to crop you image manually before using the code.
To run the jupyter notebook version of the code, enter the following into your terminal: jupyter notebook. This should open a firefox window. Navigate to the window and click on cell_counter.ipynb. You should be able to follow the instructions in the file to run the code blocks there.
Open cell_counter.py in a text editor or IDE and change filename to the name of the image you want to use. Save and run the following from your terminal: python3 cell_counter.py.