We developed four different methods for this project. The first can be described as “semi-automatic”, as it requires user-input in terms of colony radius and sensitivity setting – both of which are required input parameters for the imfindcircles function. The sensitivity parameter is vital to this project’s accuracy, as it determines the threshold at which the function will stop detecting circles. A high sensitivity setting allows for the detection of more circular objects, such as overlapping colonies or imperfectly circular colonies. Thus, a low sensitivity setting will underestimate the true number of colonies, but a high setting will overestimate the colony count.
Semi-Automatic User-Input Based Method:
- User inputs colony radius range
- Program runs through all relevant parameter combinations and displays them to the user
- User selects the best combinations
- Problem: Not automatic enough