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TreeJ: an ImageJ plugin for interactive cell lineage reconstruction from static images.

Elise Laruelle1,2,3, Jean-Christophe Palauqui4, Philippe Andrey4

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|November 17, 2023
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Summary

This study introduces TreeJ, an ImageJ/Fiji plugin for reconstructing plant cell lineages from static 3D images. It enables lineage tree generation, cell tagging, and data export for advanced analysis.

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Cell lineageImage annotationImageJ software

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Area of Science:

  • Developmental biology
  • Plant biology
  • Bioimage analysis

Background:

  • Reconstructing cell lineages is crucial in developmental biology, typically using time-lapse data.
  • Static images, often required for tissue fixation or improved staining, lack lineage information.
  • Plant cell walls preserve division history, necessitating tools for static image lineage reconstruction.

Purpose of the Study:

  • To develop a tool for generating and editing cell lineage trees from 3D labeled images.
  • To enable standardized image annotation for developmental biology research.
  • To facilitate the analysis of cell division history in static biological samples.

Main Methods:

  • Developed a user-friendly interface for building and editing lineage trees.
  • Implemented cell tagging functionality within the lineage tree structure.
  • Enabled extraction of sub-trees or cells with specific tags.

Main Results:

  • The TreeJ plugin allows users to create and modify lineage trees from 3D images.
  • Cells can be tagged, and specific cell groups can be extracted based on these tags.
  • Generated lineage trees are exportable for compatibility with other visualization and analysis software.

Conclusions:

  • TreeJ provides a solution for lineage reconstruction from static 3D images in plant biology.
  • The plugin facilitates graphical and cell pattern-level analysis of lineage trees.
  • The open-source code is available for further development and application.