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Welcome to ReLAX

This napari plugin extends the functionality of the LineageTree project by providing a comprehensive Graphical User Interface (GUI). Leveraging napari’s interactive visualization capabilities and Qt’s flexible framework, it enables users to import and explore tracking datasets, called LineageTrees directly into the Napari viewer. This project as well as LineageTree lie at the interface between graph theory and biology, thus a useful glossary was created to accomodate users who are not familiar with either of the fields

With this plugin the user has access to features like:

  • Spatial and Temporal data exploration: The user can interact with the Napari viewer and the Lineage Viewer simultaneously.

  • Node Recoloring: Recolor node colors based on lineage attributes for better insights into any dataset.

  • Unordered Tree Edit Distance Calculation: Compute pairwise distances of lineages and sublineages in datasets, to assess their similarity or dissimilarity, using Unordered Tree Edit Distance (UTED).

Here are guides available for tutorials on specific aspects of workflows available in the plugin.

This integration enhances lineage analysis by combining the powerful visualization of Napari with quantitative comparison tools in an interactive environment.

What does this combination of LineageTree and Napari offer

  • The Viewer: The spatial data are loaded into the napari viewer and can be interacted with.
  • Interaction with big datasets: Big datasets contain hundreds of annotations/nodes per chain/branch, the plugin offers the capability to explore large lineages on the interactive Lineage Viewer
  • No need for programming knowledge: This plugin does not require programming knowledge, thus comparing LineageTrees is accessible even for the untrained user.

This plugin consists of 2 components, one tailored for single dataset analysis and inspection and one for multiple dataset analysis:

  • Single dataset analysis:

    • Lineage Viewer - Explore and Relabel: Explore the lineages with its interactive Lineage Viewer, relabel lineages of interest.
    • Attribute recoloring: Recolor nodes on both the Lineage Viewer and the Napari standard Viewer, using the distance or precomputed attributes.
    • Distance Calculation: Calculate the unordered tree edit distance, inspect the distances on the Napari Standard Viewer and create histograms to compare lineages through their sublineages.

  • Multiple dataset analysis:

    • Manager: A manager to handle and save multiple embryos.
    • Cross Dataset Comparison: Easily calculate the unordered tree edit distance of lineages or sublineages across datasets.