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Cell shape characterization, alignment, and comparison using FlowShape.

Casper van Bavel1, Wim Thiels1, Rob Jelier1

  • 1Centre of Microbial and Plant Genetics, M2S Department, KU Leuven, 3001 Leuven, Belgium.

Bioinformatics (Oxford, England)
|June 16, 2023
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Summary
This summary is machine-generated.

FlowShape offers a novel framework for comprehensive cell shape analysis, moving beyond simple geometric features. This method enables detailed characterization and comparison of cell shapes, advancing biological research.

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Area of Science:

  • Cell biology
  • Biophysics
  • Computational biology

Background:

  • Cell shape is a critical indicator of cellular processes like differentiation and polarization.
  • Existing cell shape descriptors often lack completeness, focusing only on basic geometric features.
  • A need exists for a comprehensive and generic framework to analyze cell shape variations.

Purpose of the Study:

  • To introduce FlowShape, a novel computational framework for a complete and generic analysis of cell shapes.
  • To develop methods for characterizing, aligning, and statistically comparing cell shapes.
  • To apply the FlowShape framework to analyze cell shape changes in biological contexts, such as early embryonic development and gene knockdown experiments.

Main Methods:

  • Cell shapes are represented by measuring curvature and mapping it conformally onto a sphere.
  • Spherical harmonics decomposition is used to approximate the shape function for analysis.
  • The framework incorporates shape alignment using Fast Fourier Transform and statistical comparison of average shapes.

Main Results:

  • FlowShape successfully characterizes cell shapes at the seven-cell stage of the *C. elegans* embryo.
  • A filter was developed to identify cellular protrusions like lamellipodia.
  • The framework detected and quantified shape changes following Wnt pathway gene knockdown.

Conclusions:

  • FlowShape provides a powerful and versatile tool for in-depth cell shape analysis.
  • The open-source software package facilitates detailed investigation of cell morphology in various biological contexts.
  • This approach enhances the ability to link cell shape dynamics to genetic and cellular perturbations.