To run script, MATLAB software (R2018b 64-bit, MathWorks®, USA) is required. 

1. All images should be organized in subfolders  as follows:
->Parent Directory
->> Experiment_Name Folder

2. Run ImageWA.m

3. Enter the Parent Directory and choose Experiment_Name Folder

4. Specify input variabels SE_size and holes_ratio ( first try 11 and 0.1 respectively, if did not performe well change) 
(additionally strel might be changed from 'disk' to 'diamond' at single_frame_area.m, depending on the cell line used for image processing. Also, based on the image quality and brightnes treshold tresh might be adjusted. 

5. Step by step segmentation results will appear while code is running. 

6. Outputs - image and excel with WA value will be generated under the Parental Directory, Experiment_Name_current date in format dd-mm-yyyy Folder.
