Cell width

[georgeoshardo]

Hi CellModeller team!

Is there a way to change the cell width in simulations? I believe at the moment all cells are the same width.

[timrudge]

Hi Georgeos - there is a cell property "radius" (or "rad", not sure) that can be set in the same way as "length". best Tim

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On Thu, 20 Jul 2023 at 11:50, Georgeos Hardo ***@***.***> wrote: Hi CellModeller team! Is there a way to change the cell width in simulations? I believe at the moment all cells are the same width. — Reply to this email directly, view it on GitHub <#45>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABWAWAJOSBPH2D4V4BDDMKTXREEOVANCNFSM6AAAAAA2RHNZUI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[georgeoshardo]

Thank you, I will try setting it again, but if I remember from my previous attempts at working with this attribute, it is not technically possible to, say, have the daughter of a cell be a different length to its mother upon birth, correct?

[timrudge]

You can set any cell properties of daughters in the "divide" function. I wouldn't recommend changing the total length or the width very much as this could generate some big overlaps between cells and thus large forces.

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On Sun, 23 Jul 2023 at 01:35, Georgeos Hardo ***@***.***> wrote: Thank you, I will try setting it again, but if I remember from my previous attempts at working with this attribute, it is not technically possible to, say, have the daughter of a cell be a different length to its mother upon birth, correct? — Reply to this email directly, view it on GitHub <#45 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABWAWAKSROEKNVR4BJY4BFDXRRWTTANCNFSM6AAAAAA2RHNZUI> . You are receiving this because you commented.Message ID: ***@***.***>

[georgeoshardo]

Apologies for the late reply, I cannot find how to do this. No matter what I try, I cannot get cells to become wider within the simulation. Setting a new radius inside the divide function does not change the simulation output.

E.g

def divide(parent, d1, d2):
    # Specify target cell size that triggers cell division
    d1.targetVol = 3.5 + random.uniform(0.0,0.5)
    d2.targetVol = 3.5 + random.uniform(0.0,0.5)
    d1.radius = 1
    d2.radius = 1

If I print the radius at the beginning of the divide check loop, it always resets back to 0.5.

[momo12345313]

same issue, can't change cell shapes
`import random
from CellModeller.Regulation.ModuleRegulator import ModuleRegulator
from CellModeller.Biophysics.BacterialModels.CLBacterium import CLBacterium
from CellModeller.GUI.WebRenderer import WebRenderer
import numpy
import math

Maximum number of cells

max_cells = 2**15

def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=False)

regul = ModuleRegulator(sim)
# Initialize the simulator with biophysics and regulation
sim.init(biophys, regul, None, None)

# Add the two initial cells: one is a round bacterium, the other is a rod-shaped bacterium
sim.addCell(cellType=0, pos=(0, 0, 0))  # Round bacterium
sim.addCell(cellType=1, pos=(1, 0, 0))  # Rod bacterium

# Add the web renderer
renderer = WebRenderer()
sim.addRenderer(renderer)

sim.pickleSteps = 10

def init(cell):
# Specify mean and distribution of initial cell size
cell.targetVol = 2.5 + random.uniform(0.0, 0.5)

# Specify different growth rates and sizes for different cell types
if cell.cellType == 0:  # Round bacterium
    cell.growthRate = 2.0
    cell.length = 2.0  # Set round bacterium to have a shorter length
    cell.radius = 1.0  # Larger radius for round shape
else:  # Rod bacterium
    cell.growthRate = 1.5
    cell.length = 5.0  # Longer length for rod bacterium
    cell.radius = 0.5  # Smaller radius for rod shape

def update(cells):
# Iterate through each cell and flag cells that reach target size for division
for (id, cell) in cells.items():
# Set the color based on cell type
if cell.cellType == 0: # Round bacterium
cell.color = [0.6, 1.0, 0.3] # Greenish
else: # Rod bacterium
cell.color = [0.1, 0.6, 1.0] # Bluish

    # Flag for division if cell reaches target size
    if cell.volume > cell.targetVol:
        cell.divideFlag = True

def divide(parent, d1, d2):
# Specify target cell size that triggers cell division
d1.targetVol = 2.5 + random.uniform(0.0, 0.5)
d2.targetVol = 2.5 + random.uniform(0.0, 0.5)

# Assign the new cells different types based on parent type
if parent.cellType == 0:  # Round bacterium
    d1.cellType = 0
    d2.cellType = 0
    d1.length = 2.0
    d2.length = 2.0
    d1.radius = 1.0
    d2.radius = 1.0
    d1.growthRate = 2.0
    d2.growthRate = 2.0
else:  # Rod bacterium
    d1.cellType = 1
    d2.cellType = 1
    d1.length = 5.0
    d2.length = 5.0
    d1.radius = 0.5
    d2.radius = 0.5
    d1.growthRate = 1.5
    d2.growthRate = 1.5

`