Potts implementation setup

Table of Contents

• Hamiltonian terms
  • Example: Including volume and adhesion Hamiltonian terms
• Implementation parameters
  • Example: Modifying global potts parameters
  • Example: Modifying term-specific potts parameters
  • Example: Modifying term-specific potts parameters with target

The potts tag describes Cellular Potts Model (CPM) framework-specific setup. Nested tags include potts.term for Hamiltonian terms and potts.parameter for parameters.

<potts>
    <potts.term id="[ID]" />
    <potts.parameter id="[ID]" value="[VALUE]" scale="[SCALE]" />
    <potts.parameter id="[ID]" value="[VALUE]" scale="[SCALE]" term="[TERM]" />
    <potts.parameter id="[ID]" value="[VALUE]" scale="[SCALE]" term="[TERM]" target="[TARGET]" />
    ...
</potts>

Hamiltonian terms

The potts.term tag is used to specify the terms used in the CPM Hamiltonian. Valid options include:

volume

Target area (2D) or volume (3D) constraint

surface

Target perimeter (2D) or surface area (3D) constraint

height

Target height constraint (3D only)

adhesion

Adhesion contact energy (2D and 3D)

substrate

Differential substrate adhesion contact energy (3D only)

persistence

Persistence energy (2D and 3D)

To modify Hamiltonian term parameters, use the potts.parameter tag with the corresponding term attribute.

Example: Including volume and adhesion Hamiltonian terms

Specifies a Hamiltonian with the volume and adhesion terms.

<potts.term id="volume" />
<potts.term id="adhesion" />

Implementation parameters

The potts.parameter tag defines CPM implementation parameters. Unless modified, default values are used for all parameters. Defaults are listed in parameter.potts.xml.

• Either or both value and scale attributes can be applied, with value applied first
• Only numeric parameters can be modified using scale
• Parameter changes for terms can be applied to specific populations using the target attribute

ATTRIBUTE	DESCRIPTION
id	parameter name
value	new parameter value
scale	scaling factor applied to parameter value
term	Hamiltonian term the parameter applies to
target	target populations ids for the parameter

Example: Modifying global potts parameters

The MCS parameter is set to the new value of 3.

<potts.parameter id="MCS" value="3" />

Example: Modifying term-specific potts parameters

The lambda parameter in the volume term is set to the new value of 20.

<potts.parameter term="volume" id="LAMBDA" value="20" />

Example: Modifying term-specific potts parameters with target

The lambda parameter in the volume term is scaled by 2 for population A.

<potts.parameter term="volume" id="LAMBDA" scale="2" target="A" />

The adhesion between population A and population B is set to the new value of 20.

<potts.parameter term="adhesion" id="ADHESION" value="20" target="A:B" />

The adhesion between population A and the media (*) is set to the new value of 30.

<potts.parameter term="adhesion" id="ADHESION" value="30" target="A:*" />