Welcome to Tyssue’s documentation!¶

The tyssue library seeks to provide a unified interface to implement bio-mechanical models of living tissues, with a focus on epithelium modeling. It’s main focus is on vertex based models.

  • Basic creation and index manipulation
    • Easy creation of a 2D epithelial sheet
    • Datasets and specifications
    • Upcasting and downcasting data
    • Input and Output
  • Visualisation
    • Matplotlib based representation
    • Epithelial sheet representation
    • Ipyvolume based
  • Geometries
    • Planar Geometries
    • Sheet geometry in 3D
    • Monolayer
    • Bulk tissue
  • Quasistatic Models
    • Effector classes
  • Simple forward Euler solver
  • Solving from \(t = 0\) to \(t = 8\)
  • Showing the results
  • Cell Division
    • On a 2D mesh
    • Division in a 3D single layer epithelium
  • Type 1 transition
    • Type 1 transitions can also be performed on edge faces
  • Apoptosis
    • Imports
  • Core objects
    • The Epithelium object
    • Sheet object
    • Monolayer object
  • Drawing functions
    • Matplotlib based
    • Ipyvolume based
  • Geometry classes
    • Planar
    • Sheet (2D 1/2)
    • Bulk (3D)
  • Topology functions
    • Base
    • Sheet
    • Bulk and Monolayer
  • Dynamic models definitions
    • Gradients
    • Effectors and Model factory
    • Predefined models
    • Quasistatic solver
  • Epithelium generation utilities
    • Hexagonal grids
  • Input/output
    • Predefined datasets
  • Collision detection and correction
    • Detection
    • Resolution
  • Miscellanous utils
    • Decorators

Indices and tables¶

  • Index

  • Module Index

  • Search Page

Tyssue

Navigation

  • Basic creation and index manipulation
  • Visualisation
  • Geometries
  • Quasistatic Models
  • Simple forward Euler solver
  • Solving from \(t = 0\) to \(t = 8\)
  • Showing the results
  • Cell Division
  • Type 1 transition
  • Apoptosis
  • Core objects
  • Drawing functions
  • Geometry classes
  • Topology functions
  • Dynamic models definitions
  • Epithelium generation utilities
  • Input/output
  • Collision detection and correction
  • Miscellanous utils

Related Topics

  • Documentation overview
    • Next: Basic Usage of the tyssue library

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