[PSI]-CIC: A Deep-Learning Pipeline for the Annotation of Sectored Saccharomyces cerevisiae Colonies

The <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mo>[</mml:mo> <mml:mi>P</mml:mi> <mml:mi>S</mml:mi> <mml:msup><mml:mi>I</mml:mi> <mml:mo>+</mml:mo></mml:msup> <mml:mo>]</mml:mo></mml:mrow> </mml:math> prion phenotype in yeast manifests as a white, pink, or red color pigment. Experimental manipulations destabilize prion phenotypes, and allow colonies to exhibit <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mo>[</mml:mo> <mml:mi>p</mml:mi> <mml:mi>s</mml:mi> <mml:msup><mml:mi>i</mml:mi> <mml:mo>-</mml:mo></mml:msup> <mml:mo>]</mml:mo></mml:mrow> </mml:math> (red) sectored phenotypes within otherwise completely white colonies. Further investigation of the size and frequency of sectors that emerge as a result of experimental manipulation is capable of providing critical information on mechanisms of prion curing, but we lack a way to reliably extract this information. Images of experimental colonies exhibiting sectored phenotypes offer an abundance of data to help uncover molecular mechanisms of sectoring, yet the structure of sectored colonies is ignored in traditional biological pipelines. In this study, we present [PSI]-CIC, the first computational pipeline designed to identify and characterize features of sectored yeast colonies. To overcome the barrier of a lack of manually annotated data of colonies, we develop a neural network architecture that we train on synthetic images of colonies and apply to real images of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mo>[</mml:mo> <mml:mi>P</mml:mi> <mml:mi>S</mml:mi> <mml:msup><mml:mi>I</mml:mi> <mml:mo>+</mml:mo></mml:msup> <mml:mo>]</mml:mo></mml:mrow> </mml:math> , <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mo>[</mml:mo> <mml:mi>p</mml:mi> <mml:mi>s</mml:mi> <mml:msup><mml:mi>i</mml:mi> <mml:mo>-</mml:mo></mml:msup> <mml:mo>]</mml:mo></mml:mrow> </mml:math> , and sectored colonies. In hand-annotated experimental images, our pipeline correctly predicts the state of approximately 95% of colonies detected and frequency of sectors in approximately 89.5% of colonies detected. The scope of our pipeline could be extended to categorizing colonies grown under different experimental conditions, allowing for more meaningful and detailed comparisons between experiments. Our approach streamlines the analysis of sectored yeast colonies providing a rich set of quantitative metrics and provides insight into mechanisms driving the curing of prion phenotypes.