tyssue.dynamics package¶
Submodules¶
tyssue.dynamics.apoptosis_model module¶
Specific functions for apoptosis vertex model
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class
tyssue.dynamics.apoptosis_model.
ApicoBasalTension
[source]¶ Bases:
tyssue.dynamics.effectors.AbstractEffector
Effector for the apical-basal tension.
The energy is proportional to the heigth of the cell
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dimensions
= array(1.) * fJ/um**2¶
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element
= 'vert'¶
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label
= 'Apical-basal tension'¶
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magnitude
= 'radial_tension'¶
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specs
= {'vert': {'height': 1.0, 'is_active': 1, 'radial_tension': 0.0}}¶
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tyssue.dynamics.base_gradients module¶
tyssue.dynamics.bulk_gradients module¶
Base gradients for bulk geometry
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tyssue.dynamics.bulk_gradients.
lumen_volume_grad
(eptm)[source]¶ Calculates the gradient for the volume enclosed by the epithelium.
For a monolayer, it will by default compute the volume enclosed by the basal side (edges whose ‘segment’ column is “basal”). If the polarity is reversed and the apical side faces the lumen, this can be changed by setting eptm.settings[“lumen_side”] to ‘apical’
tyssue.dynamics.bulk_model module¶
Dynamical models for monlayer and bulk epithelium.
tyssue.dynamics.effectors module¶
Generic forces and energies
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class
tyssue.dynamics.effectors.
AbstractEffector
[source]¶ Bases:
object
The effector class is used by model factories to construct a model.
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dimensions
= None¶
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element
= None¶
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label
= 'Abstract effector'¶
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magnitude
= None¶
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spatial_ref
= (None, None)¶
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specs
= {'cell': {}, 'edge': {}, 'face': {}, 'vert': {}}¶
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temporal_ref
= (None, None)¶
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class
tyssue.dynamics.effectors.
BarrierElasticity
[source]¶ Bases:
tyssue.dynamics.effectors.AbstractEffector
Barrier use to maintain the tissue integrity.
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dimensions
= array(1.) * fJ/um**2¶
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element
= 'vert'¶
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label
= 'Barrier elasticity'¶
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magnitude
= 'barrier_elasticity'¶
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specs
= {'vert': {'barrier_elasticity': 1.0, 'delta_rho': 0.0, 'is_active': 1}}¶
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class
tyssue.dynamics.effectors.
BorderElasticity
[source]¶ Bases:
tyssue.dynamics.effectors.AbstractEffector
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dimensions
= array(1.) * fJ/um**2¶
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element
= 'edge'¶
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label
= 'Border edges elasticity'¶
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magnitude
= 'border_elasticity'¶
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spatial_ref
= ('prefered_length', UnitLength('micrometer', 0.001 * mm, 'um'))¶
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specs
= {'edge': {'border_elasticity': 1.0, 'is_active': 1, 'is_border': 1.0, 'length': 1.0, 'prefered_length': 1.0}}¶
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class
tyssue.dynamics.effectors.
CellAreaElasticity
[source]¶ Bases:
tyssue.dynamics.effectors.AbstractEffector
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dimensions
= array(1.) * fJ/um**4¶
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element
= 'cell'¶
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label
= 'Area elasticity'¶
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magnitude
= 'area_elasticity'¶
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spatial_ref
= ('prefered_area', array(1.) * um**2)¶
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specs
= {'cell': {'area': 1.0, 'area_elasticity': 1.0, 'is_alive': 1, 'prefered_area': 1.0}}¶
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class
tyssue.dynamics.effectors.
CellVolumeElasticity
[source]¶ Bases:
tyssue.dynamics.effectors.AbstractEffector
-
dimensions
= array(1.) * fJ/um**6¶
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element
= 'cell'¶
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label
= 'Volume elasticity'¶
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magnitude
= 'vol_elasticity'¶
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spatial_ref
= ('prefered_vol', array(1.) * um**3)¶
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specs
= {'cell': {'is_alive': 1, 'prefered_vol': 1.0, 'vol': 1.0, 'vol_elasticity': 1.0}}¶
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class
tyssue.dynamics.effectors.
FaceAreaElasticity
[source]¶ Bases:
tyssue.dynamics.effectors.AbstractEffector
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dimensionless
= False¶
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dimensions
= array(1.) * fJ/um**4¶
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element
= 'face'¶
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label
= 'Area elasticity'¶
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magnitude
= 'area_elasticity'¶
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spatial_ref
= ('prefered_area', array(1.) * um**2)¶
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specs
= {'edge': {'sub_area': 0.16666666666666666}, 'face': {'area': 1.0, 'area_elasticity': 1.0, 'is_alive': 1, 'prefered_area': 1.0}}¶
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class
tyssue.dynamics.effectors.
FaceContractility
[source]¶ Bases:
tyssue.dynamics.effectors.AbstractEffector
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dimensions
= array(1.) * fJ/um**2¶
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element
= 'face'¶
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label
= 'Contractility'¶
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magnitude
= 'contractility'¶
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spatial_ref
= ('mean_perimeter', UnitLength('micrometer', 0.001 * mm, 'um'))¶
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specs
= {'face': {'contractility': 1.0, 'is_alive': 1, 'perimeter': 1.0}}¶
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class
tyssue.dynamics.effectors.
FaceVolumeElasticity
[source]¶ Bases:
tyssue.dynamics.effectors.AbstractEffector
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dimensions
= array(1.) * fJ/um**6¶
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element
= 'face'¶
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label
= 'Volume elasticity'¶
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magnitude
= 'vol_elasticity'¶
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spatial_ref
= ('prefered_vol', array(1.) * um**3)¶
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specs
= {'edge': {'sub_area': 0.16666666666666666}, 'face': {'is_alive': 1, 'prefered_vol': 1.0, 'vol': 1.0, 'vol_elasticity': 1.0}, 'vert': {'height': 1.0}}¶
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class
tyssue.dynamics.effectors.
LengthElasticity
[source]¶ Bases:
tyssue.dynamics.effectors.AbstractEffector
Elastic half edge
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dimensions
= array(1.) * fJ/um**2¶
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element
= 'edge'¶
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label
= 'Length elasticity'¶
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magnitude
= 'length_elasticity'¶
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spatial_ref
= ('prefered_length', UnitLength('micrometer', 0.001 * mm, 'um'))¶
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specs
= {'edge': {'is_active': 1, 'length': 1.0, 'length_elasticity': 1.0, 'prefered_length': 1.0, 'ux': 0.5773502691896257, 'uy': 0.5773502691896257, 'uz': 0.5773502691896257}}¶
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class
tyssue.dynamics.effectors.
LineTension
[source]¶ Bases:
tyssue.dynamics.effectors.AbstractEffector
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dimensions
= array(1.) * fJ/um¶
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element
= 'edge'¶
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label
= 'Line tension'¶
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magnitude
= 'line_tension'¶
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spatial_ref
= ('mean_length', UnitLength('micrometer', 0.001 * mm, 'um'))¶
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specs
= {'edge': {'is_active': 1, 'line_tension': 1.0}}¶
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class
tyssue.dynamics.effectors.
LineViscosity
[source]¶ Bases:
tyssue.dynamics.effectors.AbstractEffector
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dimensions
= array(1.) * s*nN/um¶
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element
= 'edge'¶
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label
= 'Linear viscosity'¶
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magnitude
= 'edge_viscosity'¶
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spatial_ref
= ('mean_length', UnitLength('micrometer', 0.001 * mm, 'um'))¶
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specs
= {'edge': {'edge_viscosity': 1.0, 'is_active': 1}}¶
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temporal_ref
= ('dt', UnitTime('second', 's'))¶
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class
tyssue.dynamics.effectors.
LumenAreaElasticity
[source]¶ Bases:
tyssue.dynamics.effectors.AbstractEffector
..math:
rac{K_Y}{2}(A_{mathrm{lumen}} - A_{0,mathrm{lumen}})^2
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dimensions
= array(1.) * fJ/um**4¶
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element
= 'settings'¶
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label
= 'Lumen volume constraint'¶
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magnitude
= 'lumen_elasticity'¶
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spatial_ref
= ('lumen_prefered_vol', array(1.) * um**2)¶
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specs
= {'settings': {'lumen_elasticity': 1.0, 'lumen_prefered_vol': 1.0, 'lumen_vol': 1.0}}¶
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class
tyssue.dynamics.effectors.
LumenVolumeElasticity
[source]¶ Bases:
tyssue.dynamics.effectors.AbstractEffector
Global volume elasticity of the object. For example the volume of the yolk in the Drosophila embryo
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dimensions
= array(1.) * fJ/um**6¶
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element
= 'settings'¶
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label
= 'Lumen volume elasticity'¶
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magnitude
= 'lumen_vol_elasticity'¶
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spatial_ref
= ('lumen_prefered_vol', array(1.) * um**3)¶
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specs
= {'settings': {'lumen_prefered_vol': 1.0, 'lumen_vol': 1.0, 'lumen_vol_elasticity': 1.0}}¶
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class
tyssue.dynamics.effectors.
PerimeterElasticity
[source]¶ Bases:
tyssue.dynamics.effectors.AbstractEffector
From Mapeng Bi et al. https://doi.org/10.1038/nphys3471
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dimensions
= array(1.) * fJ/um**2¶
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element
= 'face'¶
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label
= 'Perimeter Elasticity'¶
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magnitude
= 'perimeter_elasticity'¶
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spatial_ref
= ('prefered_perimeter', UnitLength('micrometer', 0.001 * mm, 'um'))¶
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specs
= {'face': {'is_alive': 1, 'perimeter': 1.0, 'perimeter_elasticity': 0.1, 'prefered_perimeter': 3.81}}¶
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class
tyssue.dynamics.effectors.
RadialTension
[source]¶ Bases:
tyssue.dynamics.effectors.AbstractEffector
Apply a tension perpendicular to a face.
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dimensions
= array(1.) * fJ/um¶
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element
= 'face'¶
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label
= 'Apical basal tension'¶
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magnitude
= 'radial_tension'¶
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specs
= {'face': {'height': 1.0, 'radial_tension': 1.0}}¶
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class
tyssue.dynamics.effectors.
SurfaceTension
[source]¶ Bases:
tyssue.dynamics.effectors.AbstractEffector
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dimensions
= array(1.) * fJ/um**2¶
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element
= 'face'¶
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label
= 'Surface tension'¶
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magnitude
= 'surface_tension'¶
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spatial_ref
= ('prefered_area', array(1.) * um**2)¶
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specs
= {'face': {'area': 1.0, 'is_active': 1, 'surface_tension': 1.0}}¶
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tyssue.dynamics.factory module¶
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tyssue.dynamics.factory.
model_factory
(effectors, ref_effector=None)[source]¶ Produces a Model class with the provided effectors.
- Parameters
effectors (list of
effectors.AbstractEffectors
classes.) –ref_effector (optional, default None) – if passed, will be used for normalization, by default, the last effector in the list is used
- Returns
NewModel – methods
- Return type
a Model derived class with compute_enregy and compute_gradient
tyssue.dynamics.planar_gradients module¶
tyssue.dynamics.planar_vertex_model module¶
tyssue.dynamics.sheet_gradients module¶
Base gradients for sheet like geometries
tyssue.dynamics.sheet_vertex_model module¶
Vertex model for an Epithelial sheet (see definitions).
Depends on the sheet vertex geometry functions.
tyssue.dynamics.units module¶
Small module to manage units and dimension analysis
Module contents¶
dynamics