//This macro processes multiple images in a folder, outputting the number of bacteria pixels in the red channel and the green channel respectively to calculate the //viability of a biofilm stained with red and green viability stains. //It also saves overlay images showing the bacteria which have been detected. //See "Supplementary Information" file for details on how to run and implement the macro.
//Sophie Mountcastle (sem093@bham.ac.uk) and Nina Vyas (n.vyas@bham.ac.uk) //University of Birmingham, UK //For queries related to the original code, please contact Dr. Sarah Kuehne (s.a.kuehne@bham.ac.uk).
//In this fork, I have made the following modifications: //Updated channel analysis and protocol to work with Calcein AM (green) and TMA-DPH (blue) stains for metabolic activity and membrane integrity. //The original (SYTO9/PI) and modified (CAM/TMA-DPH) versions of the code now output the number of stained pixels instead of percentage values.
//For questions about these modifications, feel free to contact me (Tinatini.tchatchiashvili@med.uni-jena.de) //Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany