initialize_physicell_simulations#

Workflow for initializing PhysiCell simulations.

Working location structure:

(name)
├── inits
│   └── inits.PHYSICELL
│       └── (name)_(key)_(resolution).csv
└── plots
    └── plots.COORDINATES
        └── (name)_(key)_(resolution).COORDINATES.png

Initialization consist of a single cell of the specified height and volume, sampled at the given spatial resolution. Coordinates are saved to inits.PHYSICELL.

Flows

run_flow

Main initialize PhysiCell simulations flow.

run_flow(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfig) → None[source]#: Main initialize PhysiCell simulations flow.

Configs

`ContextConfig`	Context configuration for initialize PhysiCell simulations flow.
`ParametersConfig`	Parameter configuration for initialize PhysiCell simulations flow.
`SeriesConfig`	Series configuration for initialize PhysiCell simulations flow.

class ContextConfig[source]#

Context configuration for initialize PhysiCell simulations flow.

working_location: str#: Location for input and output files (local path or S3 bucket).

class ParametersConfig[source]#

Parameter configuration for initialize PhysiCell simulations flow.

grid: str = 'rect'#: Type of sampling grid (rect = rectangular, hex = hexagonal).

ds: list[float]#: Spatial scaling in um/voxel.

bounding_box: tuple[int, int] = (100, 100)#: Size of bounding box in um.

cell_height: float = 9.0#: Average cell height in um.

cell_volume: float = 1300.0#: Average cell volume in um^3.

substrate: bool = True#: True to include substrate in initialization, False otherwise.

contact_sheet: bool = True#: True to save contact sheet of initialization, False otherwise.

class SeriesConfig[source]#

Series configuration for initialize PhysiCell simulations flow.

name: str#: Name of the simulation series.