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Quantifying yeast colony morphologies with feature engineering from time-lapse photography.

Andy Goldschmidt1, James Kunert-Graf2, Adrian C Scott3

  • 1Department of Physics, University of Washington, Seattle, WA, 98195, USA. andygold@uw.edu.

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Summary

We developed a method to categorize yeast colony morphology development using image analysis. Local Binary Patterns (LBP) track texture changes, enabling clustering of Saccharomyces cerevisiae growth patterns.

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Area of Science:

  • Microbiology
  • Computational Biology
  • Image Analysis

Background:

  • Baker's yeast (Saccharomyces cerevisiae) serves as a model organism for studying multicellular colony morphology.
  • Understanding yeast colony development requires analyzing complex, time-dependent morphological changes.

Purpose of the Study:

  • To develop and apply quantitative methods for categorizing yeast colony morphology development.
  • To address statistical challenges in extracting time-dependent features from time-lapse images of yeast growth.

Main Methods:

  • Collected a dataset of time-lapse images of various Saccharomyces cerevisiae strains.
  • Utilized texture-based feature engineering, specifically Local Binary Patterns (LBP), to quantify colony surface texture.
  • Applied hierarchical clustering to group colonies based on their texture development trajectories.

Main Results:

  • Local Binary Patterns (LBP) effectively captured texture changes, showing smooth trajectories during yeast colony growth.
  • The trajectory of texture development was strain-dependent, reflecting distinct morphological emergence patterns.
  • Hierarchical clustering successfully categorized colonies based on texture trajectories, providing interpretable results.

Conclusions:

  • Texture analysis using LBP is a viable method for characterizing yeast colony morphology development.
  • Quantitative image analysis and clustering offer powerful tools for studying microbial colony morphogenesis.
  • The developed clustering approach facilitates the identification of representative colony morphologies for different growth patterns.