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