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tyssue.behaviors.sheet package

tyssue.behaviors.sheet package#

Submodules#

tyssue.behaviors.sheet.actions module#

Basic event module#

tyssue.behaviors.sheet.actions.ab_pull(sheet, face, radial_tension, distributed=False)[source]#

Adds radial_tension to the face’s vertices radial_tension

Parameters

  • sheet (a Sheet object) –

  • face (index of face) –

  • radial_tension –

  • distributed (bool: If true devide radial_tension by number of vertices,) – and apply this new radial tension to each vertices. Default not distributed.

tyssue.behaviors.sheet.actions.contract(sheet, face, contractile_increase, multiply=False, contract_col='contractility')[source]#

Contract the face by increasing the ‘contractility’ parameter by contractile_increase

Parameters

  • sheet (a Sheet object) –

  • face (index of face) –

  • contractile_increase (rate use to multiply/add value of contraction_col of face.) –

  • multiply (contractile_increase is multiply/add to the current contract_col value.) – Default False.

  • contract_col (column from face dataframe which apply contractile_increase.) – contract_col need to exist in face_df. Default ‘contractility’

tyssue.behaviors.sheet.actions.decrease(sheet, element, index, decrease_rate, col, divide=True, bound=None)[source]#

Decrease the value in the dataset at position index/col.

Parameters

  • sheet (a Sheet object) –

  • element (str: 'cell' or 'face' or 'edge' or 'vert') –

  • index (index in the datasets[element]) –

  • decrease_rate (rate use to divide value in the column col.) –

  • col (column from element which apply decrease_rate.) –

  • divide (bool: if true the current col value is divide by decrease_rate.) – If false it is substracted. Default divide.

  • bound (lower limit of the modify value. Default None.) –

tyssue.behaviors.sheet.actions.detach_vertices(sheet)[source]#

Stochastically detaches vertices from rosettes.

Uses two probabilities p_4 and p_5p stored in sheet.settings.

Parameters

sheet (a Sheet object) –

tyssue.behaviors.sheet.actions.exchange(sheet, face, geom, remove_tri_faces=True)[source]#

Execute a type1 transition on the shorter edge of a face.

Parameters

  • sheet (a Sheet object) –

  • face (index of the face) –

  • geom (a Geometry class) –

  • remove_tri_faces (remove automaticaly triangular faces if existed. Default True.) –

tyssue.behaviors.sheet.actions.grow(sheet, face, growth_rate, growth_col='prefered_vol')[source]#

Multiplies the grow columns of face by a factor.

Parameters

  • sheet (a Sheet object) –

  • face (index of face) –

  • growth_rate (rate use to multiply value of growth_col of face.) –

  • growth_col (column from face dataframe which apply growth_rate.) – growth_col need to exist in face_df. Default ‘prefered_vol’

Example

>>> print(sheet.face_df[face, 'prefered_vol'])
10
>>> grow(sheet, face, 1.7, 'prefered_vol')
>>> print(sheet.face_df[face, 'prefered_vol'])
17.0
tyssue.behaviors.sheet.actions.increase(sheet, element, index, increase_rate, col, multiply=True, bound=None)[source]#

Increase the value in the dataset at position index/col.

Parameters

  • sheet (a Sheet object) –

  • element (str: 'cell' or 'face' or 'edge' or 'vert') –

  • index (index in the datasets[element]) –

  • increase_rate (rate use to multiply value in the column col.) –

  • col (column from dataset which apply increase_rate.) –

  • multiply (bool:) – if True, the current col value is multiplied by increase_rate. if False it is added. Default True.

  • bound (Higher limit of the modify value. Default None) –

tyssue.behaviors.sheet.actions.increase_linear_tension(sheet, face, line_tension_increase, multiply=True, isotropic=True, angle=0.7853981633974483, limit=100)[source]#

Increase edges line tension from face isotropic or according to an angle.

Parameters

  • face (index of face) –

  • line_tension_increase (factor for increase line tension value) –

  • multiply (line_tension_increase is multiply or add to the current) – line_tension value. Default True.

  • isotropic (all edges are increase, or only a subset of edges. Default True.) –

  • angle (angle below edges are increase by line_tension_increase if) – isotropic is False. Default pi/4

  • limit (line_tension stay below this limit value) –

tyssue.behaviors.sheet.actions.merge_vertices(sheet)[source]#

Merges all the vertices that are closer than the threshold length

Parameters

sheet (a Sheet object) –

tyssue.behaviors.sheet.actions.remove(sheet, face, geom)[source]#

Removes the face and updates the geometry

Parameters

  • sheet (a Sheet object) –

  • face (index of the face) –

  • geom (a Geometry class) –

tyssue.behaviors.sheet.actions.set_value(sheet, element, index, set_value, col)[source]#

Set the value in the dataset at position index/col.

Parameters

  • sheet (a Sheet object) –

  • element (str: 'cell' or 'face' or 'edge' or 'vert') –

  • index (index in the datasets[element]) –

  • set_value (value to set.) –

  • col (column from dataset which apply increase_rate.) –

tyssue.behaviors.sheet.actions.shrink(sheet, face, shrink_rate, shrink_col='prefered_vol')[source]#

Devides the shrink_col of face by a factor.

Parameters

  • sheet (a Sheet object) –

  • face (index of face) –

  • shrink_rate (rate use to multiply value of shrink_col of face.) –

  • shrink_col (column from face dataframe which apply shrink_rate.) – shrink_col need to exist in face_df. Default ‘prefered_vol’

tyssue.behaviors.sheet.apoptosis_events module#

Apoptosis event module#

tyssue.behaviors.sheet.apoptosis_events.apoptosis(sheet, manager, **kwargs)[source]#

Apoptotic behavior

While the cell’s apical area is bigger than a threshold, the cell shrinks, and the contractility of its neighbors is increased. once the critical area is reached, the cell is eliminated from the apical surface through successive type 1 transition. Once only three sides are left, the cell is eliminated from the tissue.

Parameters

  • sheet (a Sheet object) –

  • manager (a EventManager object) –

  • face_id (int,) – the id of the apoptotic cell

  • shrink_rate (float, default 0.1) – the rate of reduction of the cell’s prefered volume e.g. the prefered volume is devided by a factor 1+shrink_rate

  • critical_area (area at which the face is eliminated from the sheet) –

  • radial_tension (amount of radial tension added at each contraction steps) –

  • contractile_increase (increase in contractility at the cell neighbors) –

  • contract_span (number of neighbors affected by the contracitity increase) –

  • geom (the geometry class used) –

tyssue.behaviors.sheet.basic_events module#

Small event module#

tyssue.behaviors.sheet.basic_events.check_tri_faces(sheet, manager, **kwargs)[source]#

Three neighbourghs cell elimination Add all cells with three neighbourghs in the manager to be eliminated at the next time step. :param sheet: :type sheet: a tyssue.sheet object :param manager: :type manager: a tyssue.events.EventManager object

tyssue.behaviors.sheet.basic_events.contraction(sheet, manager, **kwargs)[source]#

Single step contraction event.

tyssue.behaviors.sheet.basic_events.contraction_line_tension(sheet, manager, **kwargs)[source]#

Single step contraction event

tyssue.behaviors.sheet.basic_events.division(sheet, manager, **kwargs)[source]#

Cell division happens through cell growth up to a critical volume, followed by actual division of the face.

Parameters

  • sheet (a Sheet object) –

  • manager (an EventManager instance) –

  • face_id (int,) – index of the mother face

  • growth_rate (float, default 0.1) – rate of increase of the prefered volume

  • critical_vol (float, default 2.) – volume at which the cells stops to grow and devides

tyssue.behaviors.sheet.basic_events.face_elimination(sheet, manager, **kwargs)[source]#

Removes the face with if face_id from the sheet.

tyssue.behaviors.sheet.basic_events.reconnect(sheet, manager, **kwargs)[source]#

Performs reconnections (vertex merging / splitting) following Finegan et al. 2019

kwargs overwrite their corresponding sheet.settings entries

Keyword Arguments

  • threshold_length (the threshold length at which vertex merging is performed) –

  • p_4 (the probability per unit time to perform a detachement from a rank 4 vertex) –

  • p_5p (the probability per unit time to perform a detachement from a rank 5) – or more vertex

See also

The tricellular vertex-specific adhesion molecule Sidekick facilitates polarised cell intercalation during Drosophila axis extension _Tara M Finegan, Nathan Hervieux, Alexander Nestor-Bergmann, Alexander G. Fletcher, Guy B Blanchard, Benedicte Sanson_ bioRxiv 704932; doi: https://doi.org/10.1101/704932

tyssue.behaviors.sheet.basic_events.type1_transition(sheet, manager, **kwargs)[source]#

Custom type 1 transition event that tests if the the shorter edge of the face is smaller than the critical length.

tyssue.behaviors.sheet.delamination_events module#

Mesoderm invagination event module#

tyssue.behaviors.sheet.delamination_events.constriction(sheet, manager, **kwargs)[source]#

Constriction process This function corresponds to the process called “apical constriction” in the manuscript The cell undergoing delamination first contracts its apical area until it reaches a critical area. A probability dependent to the apical area allow an apico-basal traction of the cell. The cell can pull during max_traction time step, not necessarily consecutively. :param sheet: :type sheet: a tyssue.sheet object :param manager: :type manager: a tyssue.events.EventManager object :param face_id: the Id of the face undergoing delamination. :type face_id: int :param contract_rate: rate of increase of the face contractility. :type contract_rate: float, default 2 :param critical_area: face’s area under which the cell starts loosing sides. :type critical_area: float, default 1e-2 :param radial_tension: tension applied on the face vertices along the

apical-basal axis.

Parameters

  • contract_neighbors (bool, default False) – if True, the face contraction triggers contraction of the neighbor faces.

  • contract_span (int, default 2) – rank of neighbors contracting if contract_neighbor is True. Contraction rate for the neighbors is equal to contract_rate devided by the rank.

tyssue.behaviors.sheet.delamination_events.exchange_neighbour(sheet, manager, **kwargs)[source]#

Executes neighbour exchanges for a face: 1. if face_df[face, ‘try_collapse_edge’] is True:

collapse that face’s shortest edge into a vert

  1. if face_df[face, ‘try_expand_vert’] is True:

    expand that face’s highest-order vert into an edge

If either or both was successful: 1. Stores index of the new vert in face_df[face, ‘edge_collapsed’] 2. Stores index of the new edge in face_df[face, ‘vert_expanded’]

Parameters

  • sheet (a tyssue.sheet object) –

  • manager (a tyssue.events.EventManager object) –

  • **kwargs (parameters for the event, indices:) –

    face_id: id of the face being checked for exchange events critical_area: optional, default 1e-2,

    events are only executed if face area larger than this

    minimum_edges: optional, default 3

    edge will not be collapsed if face with fewer sides would result

    maximum_edges: optional, default 10

    vert will not be expanded if face with more sides would result

Module contents#

Sheet behavior definitions Each top level event is a series of actions leading to the completion of an event.

Contents