tyssue.generation package

Submodules

tyssue.generation.from_voronoi module

tyssue.generation.from_voronoi.from_2d_voronoi(voro, specs=None)

Creates 2D (sheet geometry) datasets from a Voronoï tessalation

Parameters

voro (a scipy.spatial.Voronoi object) –

Returns

datasets – datasets suitable for Epithelium implementation

Return type

dict

tyssue.generation.from_voronoi.from_3d_voronoi(voro)

Creates 3D (bulk geometry) datasets from a Voronoï tessalation

Parameters

voro (a scipy.spatial.Voronoi object) –

Returns

datasets – datasets suitable for Epithelium implementation

Return type

dict

Notes

It is important to reset the index of the created epithelium after creation

Example

cells = hexa_grid3d(3, 3, 3) datasets = from_3d_voronoi(Voronoi(cells)) bulk = Epithelium(‘bulk’, datasets) bulk.reset_topo() bulk.reset_index(order=True) bulk.sanitize()

tyssue.generation.hexagonal_grids module

Hexagonal grids

tyssue.generation.hexagonal_grids.circle(num_t, radius=1.0, phase=0.0)

Returns x and y positions of num_t points regularly placed around a circle of radius radius, shifted by phase radians.

Parameters

• num_t (int) – the number of points around the circle

• radius (float, default 1.) – the radius of the circle

• phase (float, default 0.0) – angle shift w/r to the x axis in radians

Returns

points

Return type

np.Ndarray of shape (num_t, 2), the x, y positions of the points

tyssue.generation.hexagonal_grids.hexa_cylinder(num_t, num_z, radius=1.0, capped=False, noise=0, orientation='transverse')

Returns an arrays of x, y positions of points evenly spread on a cylinder with num_t points on the periphery and num_z points on its length.

Parameters

• num_t (int,) – The number of points on the periphery

• num_z (int,) – The number of points along the z axis (the length of the cylinder)

• radius (float, default 1) – The radius of the cylinder

• capped (bool, default False) – If True, the tips of the cylinder are capped by a disk of point as generated by the hexa_disk function.

• noise (float, default 0) – normaly distributed position noise around the cell points

• orientation ({'transverse' | 'longitudinal'}, default 'transverse') – the orientation of the cells (with the longueur axis perpendicular or along the length of the cylinder)

tyssue.generation.hexagonal_grids.hexa_disk(num_t, radius=1)

Returns an arrays of x, y positions of points evenly spread on a disk with num_t points on the periphery.

Parameters

• num_t (int) – the number of poitns on the disk periphery, the rest of the disk is filled automaticaly

• radius (float, default 1.) – the radius of the disk

tyssue.generation.hexagonal_grids.hexa_grid2d(nx, ny, distx, disty, noise=None)

Creates an hexagonal grid of points

tyssue.generation.hexagonal_grids.hexa_grid3d(nx, ny, nz, distx=1.0, disty=1.0, distz=1.0, noise=None)

Creates an hexagonal grid of points

tyssue.generation.hexagonal_grids.three_faces_sheet(zaxis=True)

Creates the apical junctions mesh of three packed hexagonal faces. If zaxis is True (defaults to False), adds a z coordinates, with z = 0.

Faces have a side length of 1.0 +/- 1e-3.

Returns

• face_df (the faces DataFrame indexed from 0 to 2)

• vert_df (the junction vertices DataFrame)

• edge_df (the junction edges DataFrame)

tyssue.generation.hexagonal_grids.three_faces_sheet_array()

Creates the apical junctions mesh of three packed hexagonal faces. If zaxis is True (defaults to False), adds a z coordinates, with z = 0.

Faces have a side length of 1.0 +/- 1e-3.

Returns

• points ((13, ndim) np.array of floats) – the positions, where ndim is 2 or 3 depending on zaxis

• edges ((15, 2) np.array of ints) – indices of the edges

• (Nc, Nv, Ne) (triple of ints) – number of faces, vertices and edges (3, 13, 15)

tyssue.generation.modifiers module

This module provides utlities to modify an input tissue through extrusion or subdivision

tyssue.generation.modifiers.create_anchors(sheet)

Adds an edge linked to every vertices at the boundary and create anchor vertices

tyssue.generation.modifiers.extrude(apical_datasets, method='homotecy', scale=0.3, vector=[0, 0, - 1])

Extrude a sheet to form a monlayer epithelium

Parameters

• apical_datasets (*) –

• 'vert' –

• 'edge' –

• 'face' –

• method (*) –

• 'homotecy' (if method ==) –

• scale (by a factor given by) –

• scaling (the scale factor for homotetic) –

• 0.3. (default) –

• vector (*) –

• translation (used for the) –

• [0 (default) –

• 0 –

• -1] –

• 'homotecy' –

• the (the basal layer is scaled down from) –

• coordinate (apical one homoteticaly w/r to the center of the) –

• system –

• scale –

• 'translation' (if method ==) –

• from (basal vertices are translated) –

• vect (the apical ones by the vector) –

• 'normals' (if method ==) –

• from –

• vertex (the apical ones along the normal of the surface at each) –

:param : :param by a vector whose size is given by scale:

tyssue.generation.modifiers.subdivide_faces(eptm, faces)

Adds a vertex at the center of each face, and returns a new dataset

Parameters

• eptm (a Epithelium instance) –

• faces (list,) – indices of the faces to be subdivided

Returns

new_dset – a dataset with the new faces devided

Return type

dict

tyssue.generation.shapes module

class tyssue.generation.shapes.AnnularSheet(identifier, datasets, specs=None, coords=None)

Bases: Sheet

2D annular model of a cylinder-like monolayer.

Provides syntactic sugar to access the apical, basal and lateral segments of the epithlium

property apical_edges

property apical_verts

property basal_edges

property basal_verts

property lateral_edges

reset_topo()

Recomputes the number of sides for the faces and the number of faces for the cells.

segment_index(segment, element)

tyssue.generation.shapes.Lloyd_relaxation(sheet, geom, steps=10, coords=None, update_method=None)

Performs Lloyd relaxation on the sheet.

tyssue.generation.shapes.ellipse_rho(theta, a, b)

tyssue.generation.shapes.ellipsoid_sheet(a, b, c, n_zs, **kwargs)

Creates an ellipsoidal apical mesh.

Parameters

• a (floats) – Size of the ellipsoid half axes in the x, y, and z directions, respectively

• b (floats) – Size of the ellipsoid half axes in the x, y, and z directions, respectively

• c (floats) – Size of the ellipsoid half axes in the x, y, and z directions, respectively

• n_zs (int) – The (approximate) number of faces along the z axis.

• get_ellipsoid_centers (kwargs are passed to) –

Returns

• eptm (a Epithelium object)

• The mesh returned is an Epithelium and not a simpler Sheet

• so that a unique cell data can hold information on the

• whole volume of the ellipsoid.

tyssue.generation.shapes.generate_ring(Nf, R_in, R_out, R_vit=None, apical='in')

Generates a 2D tyssue object aranged in a ring of Nf tetragonal cells with inner diameter R_in and outer diameter R_out

Parameters

• Nf (int) – The number of cells in the tissue

• R_in (float) – The inner ring diameter

• R_out (float) – The outer ring diameter

• R_vit (float) – The vitelline membrane diameter (a non strechable membrane around the annulus)

• apical (str {'in' | 'out'}) – The side of the apical surface if “in”, the apical surface is inside the annulus, facing the lumen as in an organoid; if ‘out’: the apical side is facing the exterior of the tissue, as in an embryo

Returns

eptm – 2D annular tissue. The R_in and R_out parameters are stored in the class settings attribute.

Return type

AnnularSheet

tyssue.generation.shapes.get_ellipsoid_centers(a, b, c, n_zs, pos_err=0.0, phase_err=0.0)

Creates hexagonaly organized points on the surface of an ellipsoid

Parameters

• a (float) – ellipsoid radii along the x, y and z axes, respectively i.e the ellipsoid boounding box will be [[-a, a], [-b, b], [-c, c]]

• b (float) – ellipsoid radii along the x, y and z axes, respectively i.e the ellipsoid boounding box will be [[-a, a], [-b, b], [-c, c]]

• c (float) – ellipsoid radii along the x, y and z axes, respectively i.e the ellipsoid boounding box will be [[-a, a], [-b, b], [-c, c]]

• n_zs (float) – number of cells on the z axis, typical

• pos_err (float, default 0.) – normaly distributed noise of std. dev. pos_err is added to the centers positions

• phase_err (float, default 0.) – normaly distributed noise of std. dev. phase_err is added to the centers angle ϕ

tyssue.generation.shapes.sheet_from_cell_centers(points, noise=0, interp_s=0.0001)

Returns a Sheet object from the Voronoï tessalation of the cell centers.

The strategy is to project the points on a sphere, get the Voronoï tessalation on this sphere and reproject the vertices on the original (implicit) surface through linear interpolation of the cell centers.

Works for relatively smooth surfaces (at the very minimum star convex).

Parameters

• points (np.ndarray of shape (Nf, 3)) – the x, y, z coordinates of the cell centers

• noise (float, default 0.0) – addiditve normal noise stdev

• interp_s (float, default 1e-4) – interpolation smoothing factor (might need to set higher)

Returns

sheet

Return type

a Sheet object with Nf faces

tyssue.generation.shapes.spherical_monolayer(R_in, R_out, Nc, apical='out', Lloyd_relax=False)

Returns a spherical monolayer with the given inner and outer radii, and approximately the gieven number of cells.

The apical argument can be ‘in’ out ‘out’ to specify wether the apical face of the cells faces inward or outward, reespectively.

tyssue.generation.shapes.spherical_sheet(radius, Nf, Lloyd_relax=False, **kwargs)

Returns a spherical sheet with the given radius and (approximately) the given number of cells

tyssue.generation.shapes.update_on_sphere(sheet)

tyssue.generation.utils module

tyssue.generation.utils.make_df(index, spec)

Module contents

The generation module provides utilities to easily create Epithelium objects.