The techniques for counting por PCR viral detection are advancing, one way to do it is through microdroplets counting wich can be manually and a hard task and the other way is using the technology, computer vision and Machine Learning to count and obtain information to process and analyze images.
If you want to run the program by your own, wou should download the file named main.py which cointains the source code. Plus you hace to download as some images to test it out.