Geometry Overview

There are 2 types of geometries in VCell, spatial and non-spatial:

Non-spatial geometries (0 dimensional and not spatially resolved) are implicitly defined in non-spatial applications (for ODE and non-spatial stochastic simulations).
Spatial geometries (1,2,3 dimensional and spatially resolved) must be explicitly defined by the user in spatial applications (for PDE and spatial stochastic simulations).

Spatial geometries can be defined in several ways:

Re-using previously defined geometries from other VCell model applications (including shared models from other users).
Creating new geometries by defining analytic equations that describe compartment distributions in space. (Analytic Geometry)
Creating new geometries by manually defining compartments on a regular grid of points in space (image painting). (Image Geometry)
Creating new geometries by importing pre-segmented image files defining compartments as areas of different pixel values. (Image Geometry)
Creating new geometries by importing image files as templates and performing image processing functions to define compartments. (Image Geometry)
Creating new geometries by importing surface mesh files and sampling within a spatial domain to define compartments. (Geometry from Surface)

Geometries can be viewed as:

Individual image planes in the x,y,z dimension.
Rendered surface boundaries between compartment regions.

The Geometry domain (origin and extent) can be edited. The geometry can be exported in different surface mesh formats by clicking the Export... button. Analytic geometries functions can be edited in place by double-clicking the table cell containing the analytic expression. An analytic geometry can be converted to an Image Geometry by clicking the Edit Image button. The currently defined geometry can be changed (replaced).