HYPHAEdelity: a quantitative image analysis tool for assessing peripheral whole colony filamentation

Scott J. Britton*, Lisa Rogers, Jane S. White, Dawn Louise Maskell

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)
12 Downloads (Pure)


The yeast Saccharomyces cerevisiae, also known as brewer's yeast, can undergo a reversible stress-responsive transition from individual ellipsoidal cells to chains of elongated cells in response to nitrogen- or carbon starvation. Whole colony morphology is frequently used to evaluate phenotypic switching response; however, quantifying two-dimensional top-down images requires each pixel to be characterized as belonging to the colony or background. While feasible for a small number of colonies, this labor-intensive assessment process is impracticable for larger datasets. The software tool HYPHAEdelity has been developed to semi-automate the assessment of two-dimensional whole colony images and quantify the magnitude of peripheral whole colony yeast filamentation using image analysis tools intrinsic to the OpenCV Python library. The software application functions by determining the total area of filamentous growth, referred to as the f-measure, by subtracting the area of the inner colony boundary from the outer-boundary area associated with hyphal projections. The HYPHAEdelity application was validated against automated and manually pixel-counted two-dimensional top-down images of S. cerevisiae colonies exhibiting varying degrees of filamentation. HYPHAEdelity's f-measure results were comparable to areas determined through a manual pixel enumeration method and found to be more accurate than other whole colony filamentation software solutions.
Original languageEnglish
Article numberfoac060
JournalFEMS Yeast Research
Issue number1
Early online date18 Nov 2022
Publication statusPublished - 2022


  • Carbon
  • Filamentous Growth
  • Gene Library
  • Hyphae
  • Image Processing, Computer-Assisted
  • Image analysis
  • Morphogenesis
  • Phenotypic Switching
  • Pseudohyphal Differentiation
  • Saccharomyces cerevisiae
  • Whole Colony Morphology
  • Yeast


Dive into the research topics of 'HYPHAEdelity: a quantitative image analysis tool for assessing peripheral whole colony filamentation'. Together they form a unique fingerprint.

Cite this