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Griottes: a generalist tool for network generation from segmented tissue images.

Gustave Ronteix1,2, Andrey Aristov1, Valentin Bonnet1,2

  • 1Institut Pasteur, Université Paris Cité, Physical microfluidics and Bioengineering, Paris, F-75015, France.

BMC Biology
|August 11, 2022
PubMed
Summary

Griottes is an open-source tool that creates a network twin of biological tissues from microscopy images. This tool extracts cell behaviors and interactions, offering multi-scale biological insights efficiently.

Keywords:
GraphsImage analysisNapariPythonSingle-cell imagingSpatial analysisTissue imaging

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Area of Science:

  • Computational Biology
  • Bioimaging
  • Systems Biology

Background:

  • Advances in microscopy and image segmentation generate vast biological image data.
  • Increased reliance on imaging necessitates efficient methods for extracting cellular behavior and interaction information.
  • Current methods require significant computational power for organizing complex biological image data.

Purpose of the Study:

  • Introduce Griottes, an open-source tool for creating network representations of biological tissues from microscopy images.
  • Enable extraction of biologically relevant metrics on individual cells and their neighborhoods.
  • Provide multi-scale biological insights from 2D and 3D tissue imaging data.

Main Methods:

  • Develop Griottes as an open-source library for building "network twins" from segmented microscopy images.
  • Encode cells and their properties as nodes and neighborhood interactions as links in a network representation.
  • Demonstrate the library's capabilities on diverse image and data types.

Main Results:

  • Griottes successfully builds network representations of 2D and 3D tissues.
  • The tool provides a wide range of biologically relevant metrics for cells and their neighborhoods.
  • Multi-scale biological insights are achievable through the network twin approach.

Conclusions:

  • Griottes is an open-source tool designed for biological image analysis.
  • The library can be integrated into existing image analysis workflows to enhance their capabilities.
  • Facilitates efficient extraction and analysis of complex cellular interaction data.