Raspberry Pi Petri Dish Cell Counter This is a small program used to count the colonies formed in a petri dish. The main purpose is to identify the colonies, and then calculate the area of the colonies over time so that a growth curve can be established.
The progam was created as part of a school project focused on making a development in microbiology.
To Run: Have the test2 m file and the countCFU function in the same workspace. Follow Instructions here to setup hardware. https://www.mathworks.com/hardware-support/raspberry-pi-matlab.html Run test2 To Modify: To alter how many pictures are taken, alter the for loop in the test2 file The program is currently set to read bright objects on a darker background. To read dark objects on a bright background, change line 23 to: [centersBright, radiiBright] = imfindcircles(cells,[1 15],'ObjectPolarity','dark','Sensitivity',.75);
Notes
Hardware Used: Raspberry Pi 3 Model B Rasberry Pi Camera Module V2
Software Used: Matlab 2016b Raspberry Pi drive was flashed with a specific version of rasbian that allowed easy communication between Matlab and the master computer computer