Script to detect droplets (circular bright spots) in 2D images, originally by Jonathan Henninger.
To run the script, you'll need to install the following packages:
numpy, matplotlib, pandas, xlsxwriter, scikit-image, opencv
A snapshot of my Anaconda environment can be found in the environment.yml file.
You need a folder containing the files and each condition in subfolders:
Script > condition 1 > all images from condition 1
> condition 2 > all images from condition 2
> condition 3 > all images from condition 3
Every image needs to be present twice: once as ND2 file, once as TIFF file. The TIFF file can have multiple channels, stored as CYX.
If you got the images from a different microscope without nd2 extension, you need to change it on the files. Just ctrl + F "Nd2" and swap for whatever file extension you have
To run the script, open Anaconda Prompt and run the following code:
python main.py pathtofolder pathtooutput
See IN VITRO DROPLET INSTRUCTIONS.txt for optional parameters.