Complex Colony Morphology (CCM) Scale: Integer CCM scale by which biofilms were scored from “0” to “5”.
Descriptions
CCM Quantification Scale:
Score 0: No growth.
Score 1: Colony with no CCM.
Score 2: Colony with low levels of CCM.
Score 3: Colony with moderate levels of CCM.
Score 4: Colony with high levels of CCM.
Score 5: Colony with extremely high levels of CCM.
Phenotyping Approach:
The CCM phenotype was assayed using three different solid agar media in OmniTrays (Nunc 264728): (1) yeast-peptone-low-dextrose (YPLD) medium (1% yeast extract, 2% peptone, 2% agar, 0.1% dextrose), (2) yeast-peptone-low-ethanol (YP-LEthanol) (1% yeast extract, 2% peptone, 2% agar, 0.5% ethanol), and (3) YPD. The first two media created low carbon environments, while the third was a rich environment meant to be a control. The CCM plates were imaged after 5 days of 30C incubation using an Epson Expression 11000 XL scanner. This site displays only CCM phenotypes scored from LD plate images.
The CCM phenotypes are quantified using a convolutional neural network categorization model; the original code for this model is available here.