def basic_simulation(cells, force, dt=dt, T1_eps=0.04):
while True:
cells.mesh, number_T1 = cells.mesh.transition(T1_eps)
F = force(cells) / viscosity
expansion = 0.05 * np.average(F * cells.mesh.vertices, 1) * dt
dv = dt * model.sum_vertices(cells.mesh.edges, F)
cells.mesh = cells.mesh.moved(dv).scaled(1.0 + expansion)
yield cells
def simulation_with_division(
cells,
force,
dt=dt,
T1_eps=T1_eps,
lifespan=100.0,
rand=None): #(cells,force,dt=0.001,T1_eps=0.04,lifespan=100.0,rand=Non
properties = cells.properties
properties[
'parent'] = cells.mesh.face_ids #save the ids to control division parents-daugthers
properties['ageingrate'] = np.random.normal(
1.0 / lifespan, 0.2 / lifespan,
len(cells)) #degradation rate per each cell
properties['ids_division'] = [
] #save ids of the cell os the division when it's ready per each time step
properties['force_x'] = []
properties['force_y'] = []
properties['T1_angle_pD'] = []
properties['Division_angle_pD'] = []
expansion = np.array([0.0, 0.0])
while True:
#cells id where is true the division conditions: living cells & area greater than 2 & age cell in mitosis
ready = np.where(~cells.empty() & (cells.mesh.area >= A_c)
& (cells.properties['age'] >= (t_G1 + t_S + t_G2)))[0]
if len(
ready
): #these are the cells ready to undergo division at the current timestep
properties['ageingrate'] = np.append(
properties['ageingrate'],
np.abs(
np.random.normal(1.0 / lifespan, 0.2 / lifespan,
2 * len(ready))))
properties['age'] = np.append(properties['age'],
np.zeros(2 * len(ready)))
properties['parent'] = np.append(
properties['parent'],
np.repeat(properties['parent'][ready],
2)) # Daugthers and parent have the same ids
properties['ids_division'] = ready
edge_pairs = [
division_axis(cells.mesh, cell_id, rand) for cell_id in ready
] #New edges after division
cells.mesh = cells.mesh.add_edges(
edge_pairs) #Add new edges in the mesh
for i in range(len(ready)):
commun_edges = np.intersect1d(
cells.mesh.length[np.where(
cells.mesh.face_id_by_edge == (cells.mesh.n_face - 2 *
(i + 1)))[0]],
cells.mesh.length[np.where(
cells.mesh.face_id_by_edge == (cells.mesh.n_face - 1 -
2 * i))[0]])
division_new_edge = np.where(
cells.mesh.length == np.max(commun_edges))[0]
properties['Division_angle_pD'] = np.append(
properties['Division_angle_pD'],
cells.mesh.edge_angle[division_new_edge][0])
properties['age'] = properties['age'] + dt * properties[
'ageingrate'] #add time step depending of the degradation rate
"""Calculate z nuclei position (Apical-Basal movement), depending of the cell cycle phase time and age of the cell"""
N_G1 = 1 - 1.0 / t_G1 * properties['age'] #nuclei position in G1 phase
N_S = 0
N_G2 = 1.0 / (t_G2) * (properties['age'] - (t_G1 + t_S)
) #nuclei position in G2 and S phase
properties['zposn'] = np.minimum(
1.0, np.maximum(N_G1, np.maximum(N_S, N_G2)))
"""Target area function depending age and z nuclei position"""
properties['A0'] = (properties['age'] +
1.0) * 0.5 * (1.0 + properties['zposn']**2)
#############BAETTI VID
#ath BAETTI D VID
cells.mesh, number_T1, d = cells.mesh.transition(
T1_eps) #check edges verifing T1 transition
if len(number_T1) > 0:
for ii in number_T1:
index = cells.mesh.face_id_by_edge[ii]
properties['T1_angle_pD'] = np.append(
properties['T1_angle_pD'], cells.mesh.edge_angle[ii])
F = force(
cells
) / viscosity #force per each cell force= targetarea+Tension+perimeter+pressure_boundary
#EG BAETTI VID
len_modified = np.matrix.copy(cells.mesh.length)
#len_modified[np.where((properties['parent_group'][cells.mesh.face_id_by_edge]==1) & np.logical_not(properties['parent_group'][cells.mesh.face_id_by_edge[cells.mesh.edges.reverse]]==0))]*=0.12
tens = (0.5 * cells.by_edge('Lambda', 'Lambda_boundary') /
len_modified) * cells.mesh.edge_vect
tens = tens - tens.take(cells.mesh.edges.prev, 1)
F += tens
dv = dt * model.sum_vertices(
cells.mesh.edges,
F) #movement of the vertices using eq: viscosity*dv/dt = F
properties['force_x'] = F[0] * viscosity
properties['force_y'] = F[1] * viscosity
if hasattr(cells.mesh.geometry, 'width'):
expansion[0] = expansion_constant * np.average(
F[0] *
cells.mesh.vertices[0]) * dt / (cells.mesh.geometry.width**2)
if hasattr(cells.mesh.geometry,
'height'): #Cylinder mesh doesn't have 'height' argument
expansion[1] = np.average(F[1] * cells.mesh.vertices[1]) * dt / (
cells.mesh.geometry.height**2)
cells.mesh = cells.mesh.moved(dv).scaled(1.0 + expansion)
yield cells
def simulation_with_division_clone_differenciation_3stripes(
cells,
force,
dt=dt,
T1_eps=T1_eps,
lifespan=100.0,
rand=None): #(cells,force,dt=0.001,T1_eps=0.04,lifespan=100.0,rand=Non
properties = cells.properties
properties[
'parent'] = cells.mesh.face_ids #save the ids to control division parents-daugthers
properties['ageingrate'] = np.random.normal(
1.0 / lifespan, 0.2 / lifespan,
len(cells)) #degradation rate per each cell
#floor plate cells
no = len(
properties['ageingrate'][np.where(properties['parent_group'] == 3)])
properties['ageingrate'][np.where(
properties['parent_group'] == 3)] = np.random.normal(
0.5 / lifespan, 0.1 / lifespan, no)
properties['ids_division'] = [
] #save ids of the cell os the division when it's ready per each time step
properties['ids_division_1'] = [
] #save ids of the cell os the division when it's ready per each time step and region
properties['ids_division_02'] = [
] #save ids of the cell os the division when it's ready per each time step and region
properties['poisoned'] = np.zeros(
len(cells)) ### to add diferenciation rate in PMN
# properties['differentiation_rate']= np.zeros(len(cells),dtype=int)
properties['force_x'] = []
properties['force_y'] = []
properties['T1_angle_pMN'] = []
properties['T1_angle_pD'] = []
properties['Division_angle_pMN'] = []
properties['Division_angle_pD'] = []
properties['deleted_edges'] = []
properties['edges_division'] = []
properties['T1_edge'] = []
expansion = np.array([0.0, 0.0])
while True:
#cells id where is true the division conditions: living cells & area greater than 2 & age cell in mitosis
ready = np.where(
(~cells.empty() & (cells.mesh.area >= A_c)
& (cells.properties['age'] >= (t_G1 + t_S + t_G2)))
| (~cells.empty() & (cells.properties['parent_group'] == 3)
& (cells.mesh.area >= 0.4)
& (cells.properties['age'] >= (t_G1 + t_S + t_G2))))[0]
if len(
ready
): #these are the cells ready to undergo division at the current timestep
#properties['ageingrate'] =np.append(properties['ageingrate'], np.repeat(properties['ageingrate'][ready],2))
properties['age'] = np.append(properties['age'],
np.zeros(2 * len(ready)))
properties['parent'] = np.append(
properties['parent'],
np.repeat(properties['parent'][ready],
2)) # Daugthers and parent have the same ids
properties['ids_division'] = ready
properties['parent_group'] = np.append(
properties['parent_group'],
np.repeat(properties['parent_group'][ready],
2)) #use to draw clones
properties['poisoned'] = np.append(
properties['poisoned'], np.zeros(
2 * len(ready))) ### to add diferenciation rate in PMN
edge_pairs = [
division_axis(cells.mesh, cell_id, rand) for cell_id in ready
] #New edges after division
properties['edges_division'].append(edge_pairs)
cells.mesh = cells.mesh.add_edges(
edge_pairs) #Add new edges in the mesh
for i in range(len(ready)):
commun_edges = np.intersect1d(
cells.mesh.length[np.where(
cells.mesh.face_id_by_edge == (cells.mesh.n_face - 2 *
(i + 1)))[0]],
cells.mesh.length[np.where(
cells.mesh.face_id_by_edge == (cells.mesh.n_face - 1 -
2 * i))[0]])
division_new_edge = np.where(
cells.mesh.length == np.max(commun_edges))[0]
if properties['parent_group'][ready[i]] == 3:
properties['ageingrate'] = np.append(
properties['ageingrate'],
np.abs(
np.random.normal(1.0 / lifespan, 0.2 / lifespan,
2)))
else:
properties['ageingrate'] = np.append(
properties['ageingrate'],
np.abs(
np.random.normal(1.0 / lifespan, 0.2 / lifespan,
2)))
# print len(properties['ageingrate'])
#if properties['parent_group'][cells.mesh.n_face-2*(i+1)]==1:
# properties['Division_angle_pMN']= np.append(properties['Division_angle_pMN'],cells.mesh.edge_angle[division_new_edge][0])
#else:
# properties['Division_angle_pD']= np.append(properties['Division_angle_pD'],cells.mesh.edge_angle[division_new_edge][0])
#for ids in ready:
# if properties['parent_group'][ids]==1:
# properties['ids_division_1'] = np.append(properties['ids_division_1'], ids)
# else:
# properties['ids_division_02'] = np.append(properties['ids_division_02'], ids)
###### Differentiation rate
properties['differentiation_rate'] = time_hours * dt * (np.array([
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
]))[properties['parent_group']] #Used 0.02, 0.0002 & 1/13
properties['poisoned'] = properties['poisoned'] - (
properties['poisoned'] -
1) * (~(cells.empty()) &
(rand.rand(len(cells)) < properties['differentiation_rate']))
properties['age'] = properties['age'] + dt * properties[
'ageingrate'] #add time step depending of the degradation rate
N_G1 = 1 - 1.0 / t_G1 * properties['age'] #nuclei position in G1 phase
N_S = 0
N_G2 = 1.0 / (t_G2) * (properties['age'] - (t_G1 + t_S)
) #nuclei position in G2 and S phase
properties['zposn'] = np.minimum(
1.0, np.maximum(N_G1, np.maximum(N_S, N_G2)))
properties['zposn'][np.where(properties['parent_group'] == 3)] = 0
"""Target area function depending age and z nuclei position"""
properties['A0'] = (properties['age'] + 1.0) * 0.5 * (
1.0 + properties['zposn']**2) * (1.0 -
cells.properties['poisoned'])
cells.mesh, number_T1, del_edges = cells.mesh.transition(T1_eps)
properties['deleted_edges'].append(del_edges)
#if len(number_T1)>0:
# for ii in number_T1:
# properties['T1_edge']=np.append(properties['T1_edge'], ii)
# index = cells.mesh.face_id_by_edge[ii]
#if properties['parent_group'][index]==1:
# properties['T1_angle_pMN'] =np.append(properties['T1_angle_pMN'],cells.mesh.edge_angle[ii])
#else:
# properties['T1_angle_pD'] =np.append(properties['T1_angle_pD'],cells.mesh.edge_angle[ii])
F = force(
cells
) / viscosity #force per each cell force= targetarea+Tension+perimeter+pressure_boundary
#ADDING THE FLOOR PLATE
len_modified = np.matrix.copy(cells.mesh.length)
#this next line can be use for modifying all edges at the boundary
#len_modified[np.where( ((properties['parent_group'][cells.mesh.face_id_by_edge]==3) & np.logical_not(properties['parent_group'][cells.mesh.face_id_by_edge[cells.mesh.edges.reverse]]==3)) | ((properties['parent_group'][cells.mesh.face_id_by_edge]==2) & (properties['parent_group'][cells.mesh.face_id_by_edge[cells.mesh.edges.reverse]]==3)) | ((properties['parent_group'][cells.mesh.face_id_by_edge]==4) & (properties['parent_group'][cells.mesh.face_id_by_edge[cells.mesh.edges.reverse]]==3)) )]*=0.004
#modifying tension w.r.t. area
for n in np.where(
((properties['parent_group'][cells.mesh.face_id_by_edge] == 3)
& np.logical_not(
properties['parent_group'][cells.mesh.face_id_by_edge[
cells.mesh.edges.reverse]] == 3)))[0]:
if abs(cells.mesh.area[cells.mesh.face_id_by_edge[n]] -
cells.mesh.area[cells.mesh.face_id_by_edge[
cells.mesh.edges.reverse[n]]]) > 0.4:
len_modified[n] *= 0.002
tens = (0.5 * cells.by_edge('Lambda', 'Lambda_boundary') /
len_modified) * cells.mesh.edge_vect
tens = tens - tens.take(cells.mesh.edges.prev, 1)
F += tens
dv = dt * model.sum_vertices(
cells.mesh.edges,
F) #movement of the vertices using eq: viscosity*dv/dt = F
#properties['force_x'] = F[0]*viscosity
#properties['force_y'] = F[1]*viscosity
if hasattr(cells.mesh.geometry, 'width'):
expansion[0] = expansion_constant * np.average(
F[0] *
cells.mesh.vertices[0]) * dt / (cells.mesh.geometry.width**2)
if hasattr(cells.mesh.geometry,
'height'): #Cylinder mesh doesn't have 'height' argument
expansion[1] = np.average(F[1] * cells.mesh.vertices[1]) * dt / (
cells.mesh.geometry.height**2)
cells.mesh = cells.mesh.moved(dv).scaled(1.0 + expansion)
yield cells
def simulation_with_division_clone_whole_tissue_differenciation(
cells,
force,
dt=dt,
T1_eps=T1_eps,
lifespan=100.0,
rand=None
): #(cells,force,dt=0.001,T1_eps=0.04,lifespan=100.0,rand=None
properties = cells.properties
properties[
'parent'] = cells.mesh.face_ids #save the ids to control division parents-daugthers
properties['ageingrate'] = np.random.normal(
1.0 / lifespan, 0.2 / lifespan,
len(cells)) #degradation rate per each cell
properties['ids_division'] = [
] #save ids of the cell os the division when it's ready per each time step
properties['ids_division_1'] = [
] #save ids of the cell os the division when it's ready per each time step and region
properties['ids_division_02'] = [
] #save ids of the cell os the division when it's ready per each time step and region
properties['poisoned'] = np.zeros(
len(cells)) ### to add diferenciation rate in PMN
# properties['differentiation_rate']= np.zeros(len(cells),dtype=int)
properties['force_x'] = []
properties['force_y'] = []
properties['T1_angle_pMN'] = []
properties['T1_angle_pD'] = []
properties['Division_angle_pMN'] = []
properties['Division_angle_pD'] = []
properties['ids_removed'] = []
expansion = np.array([0.0, 0.0])
while True:
#cells id where is true the division conditions: living cells & area greater than 2 & age cell in mitosis
ready = np.where(~cells.empty() & (cells.mesh.area >= A_c)
& (cells.properties['age'] >= (t_G1 + t_S + t_G2)))[0]
if len(
ready
): #these are the cells ready to undergo division at the current timestep
properties['ageingrate'] = np.append(
properties['ageingrate'],
np.abs(
np.random.normal(1.0 / lifespan, 0.2 / lifespan,
2.0 * len(ready))))
properties['age'] = np.append(properties['age'],
np.zeros(2 * len(ready)))
properties['parent'] = np.append(
properties['parent'],
np.repeat(properties['parent'][ready],
2)) # Daugthers and parent have the same ids
properties['ids_division'] = ready
properties['parent_group'] = np.append(
properties['parent_group'],
np.repeat(properties['parent_group'][ready],
2)) #use to draw clones
properties['poisoned'] = np.append(
properties['poisoned'], np.zeros(
2 * len(ready))) ### to add diferenciation rate in PMN
# properties['differentiation_rate'] = np.append(properties['differentiation_rate'], diff_rate_hours*np.ones(2*len(ready)))
edge_pairs = [
division_axis(cells.mesh, cell_id, rand) for cell_id in ready
] #New edges after division
cells.mesh = cells.mesh.add_edges(
edge_pairs) #Add new edges in the mesh
for i in range(len(ready)):
commun_edges = np.intersect1d(
cells.mesh.length[np.where(
cells.mesh.face_id_by_edge == (cells.mesh.n_face - 2 *
(i + 1)))[0]],
cells.mesh.length[np.where(
cells.mesh.face_id_by_edge == (cells.mesh.n_face - 1 -
2 * i))[0]])
division_new_edge = np.where(
cells.mesh.length == np.max(commun_edges))[0]
if properties['parent_group'][cells.mesh.n_face - 2 *
(i + 1)] == 1:
properties['Division_angle_pMN'] = np.append(
properties['Division_angle_pMN'],
cells.mesh.edge_angle[division_new_edge][0])
else: #antes estaba mal y ponia pD!!!! las simulaciones guardadas estan mal
properties['Division_angle_pMN'] = np.append(
properties['Division_angle_pMN'],
cells.mesh.edge_angle[division_new_edge][0])
for ids in ready:
if properties['parent_group'][ids] == 1:
properties['ids_division_1'] = np.append(
properties['ids_division_1'], ids)
else: #antes estaba mal y ponia 0_2!!!! las simulaciones guardadas estan mal
properties['ids_division_1'] = np.append(
properties['ids_division_1'], ids)
###### Defferentiation rate
properties['differentiation_rate'] = time_hours * dt * (np.array([
0.0, diff_rate_hours, 0.0, 0.0, 0.0, diff_rate_hours, 0.0
]))[properties['parent_group']] #Used 0.02, 0.0002 & 1/13
properties['poisoned'] = properties['poisoned'] - (
properties['poisoned'] -
1) * (~(cells.empty()) &
(rand.rand(len(cells)) < properties['differentiation_rate']))
properties['age'] = properties['age'] + dt * properties[
'ageingrate'] #add time step depending of the degradation rate
N_G1 = 1 - 1.0 / t_G1 * properties['age'] #nuclei position in G1 phase
N_S = 0
N_G2 = 1.0 / (t_G2) * (properties['age'] - (t_G1 + t_S)
) #nuclei position in G2 and S phase
properties['zposn'] = np.minimum(
1.0, np.maximum(N_G1, np.maximum(N_S, N_G2)))
"""Target area function depending age and z nuclei position"""
properties['A0'] = (properties['age'] + 1.0) * 0.5 * (
1.0 + properties['zposn']**2) * (1.0 -
cells.properties['poisoned'])
cells.mesh, number_T1, ids_removed = cells.mesh.transition(T1_eps)
properties['ids_removed'].append(ids_removed) #####BAETTI VID
if len(number_T1) > 0:
for ii in number_T1:
index = cells.mesh.face_id_by_edge[ii]
if properties['parent_group'][index] == 1:
properties['T1_angle_pMN'] = np.append(
properties['T1_angle_pMN'], cells.mesh.edge_angle[ii])
else: #antes estaba mal y ponia pD!!!! las simulaciones guardadas estan mal
properties['T1_angle_pMN'] = np.append(
properties['T1_angle_pMN'], cells.mesh.edge_angle[ii])
F = force(
cells
) / viscosity #force per each cell force= targetarea+Tension+perimeter+pressure_boundary
dv = dt * model.sum_vertices(
cells.mesh.edges,
F) #movement of the vertices using eq: viscosity*dv/dt = F
properties['force_x'] = F[0] * viscosity
properties['force_y'] = F[1] * viscosity
if hasattr(cells.mesh.geometry, 'width'):
expansion[0] = expansion_constant * np.average(
F[0] *
cells.mesh.vertices[0]) * dt / (cells.mesh.geometry.width**2)
if hasattr(cells.mesh.geometry,
'height'): #Cylinder mesh doesn't have 'height' argument
expansion[1] = np.average(F[1] * cells.mesh.vertices[1]) * dt / (
cells.mesh.geometry.height**2)
cells.mesh = cells.mesh.moved(dv).scaled(1.0 + expansion)
yield cells
def simulation_with_division_clone_differentiation(
cells,
force,
dt=dt,
T1_eps=T1_eps,
lifespan=100.0,
rand=None): #(cells,force,dt=0.001,T1_eps=0.04,lifespan=100.0,rand=Non
properties = cells.properties
properties[
'parent'] = cells.mesh.face_ids #save the ids to control division parents-daugthers
properties['ageingrate'] = np.random.normal(
1.0 / lifespan, 0.2 / lifespan,
len(cells)) #degradation rate per each cell
properties['ids_division'] = [
] #save ids of the cell os the division when it's ready per each time step
properties['poisoned'] = np.zeros(
len(cells)) ### to add diferenciation rate in PMN
expansion = np.array([0.0, 0.0])
while True:
#cells id where is true the division conditions: living cells & area greater than 2 & age cell in mitosis
ready = np.where(~cells.empty() & (cells.mesh.area >= A_c)
& (cells.properties['age'] >= (t_G1 + t_S + t_G2)))[0]
if len(
ready
): #these are the cells ready to undergo division at the current timestep
properties['ageingrate'] = np.append(
properties['ageingrate'],
np.abs(
np.random.normal(1.0 / lifespan, 0.2 / lifespan,
2.0 * len(ready))))
properties['age'] = np.append(properties['age'],
np.zeros(2 * len(ready)))
properties['parent'] = np.append(
properties['parent'],
np.repeat(properties['parent'][ready],
2)) # Daugthers and parent have the same ids
properties['ids_division'] = ready
properties['parent_group'] = np.append(
properties['parent_group'],
np.repeat(properties['parent_group'][ready],
2)) #use to draw clones
properties['poisoned'] = np.append(
properties['poisoned'], np.zeros(
2 * len(ready))) ### to add diferenciation rate in PMN
edge_pairs = [
division_axis(cells.mesh, cell_id, rand) for cell_id in ready
] #New edges after division
cells.mesh = cells.mesh.add_edges(
edge_pairs) #Add new edges in the mesh
###### Defferenciation rate
properties['poisoned'] = properties['poisoned'] - (
properties['poisoned'] -
1) * (~(cells.empty()) & (rand.rand(len(cells)) <
(dt * diff_rate_hours * time_hours)))
properties['age'] = properties['age'] + dt * properties[
'ageingrate'] #add time step depending of the degradation rate
"""Calculate z nuclei position (Apical-Basal movement), depending of the cell cycle phase time and age of the cell"""
N_G1 = 1 - 1.0 / t_G1 * properties['age'] #nuclei position in G1 phase
N_S = 0
N_G2 = 1.0 / (t_G2) * (properties['age'] - (t_G1 + t_S)
) #nuclei position in G2 and S phase
properties['zposn'] = np.minimum(
1.0, np.maximum(N_G1, np.maximum(N_S, N_G2)))
"""Target area function depending age and z nuclei position"""
properties['A0'] = (properties['age'] + 1.0) * 0.5 * (
1.0 + properties['zposn']**2) * (1.0 -
cells.properties['poisoned'])
cells.mesh, number_T1 = cells.mesh.transition(
T1_eps) #check edges verifing T1 transition
F = force(
cells
) / viscosity #force per each cell force= targetarea+Tension+perimeter+pressure_boundary
dv = dt * model.sum_vertices(
cells.mesh.edges,
F) #movement of the vertices using eq: viscosity*dv/dt = F
if hasattr(cells.mesh.geometry, 'width'):
expansion[0] = expansion_constant * np.average(
F[0] *
cells.mesh.vertices[0]) * dt / (cells.mesh.geometry.width**2)
if hasattr(cells.mesh.geometry,
'height'): #Cylinder mesh doesn't have 'height' argument
expansion[1] = np.average(F[1] * cells.mesh.vertices[1]) * dt / (
cells.mesh.geometry.height**2)
cells.mesh = cells.mesh.moved(dv).scaled(1.0 + expansion)
yield cells