The lattice in CC3D represents a coordinate space in which you can measure positions. or measurements in length (in voxels). The other thing you can visualize from your simulation are measurements in time (in mcs) by observing how your configuration is changing. These length or time values are only a representation . For example, I could have a cell which measures 15 microns in diameter. To represent it I can construct a cell in CC3D with a diameter of 15 voxels and now my scale would be 1 voxel=1 micron. I could also pick a smaller or larger simulation diameter and scale accordingly.
Similarly I could have a problem in which my cell grows, reaches twice its volume and divides. If I know experimentally that the cell division time is 100 minutes, I would from my simulation check how long it takes for its growth and division and relate that mcs value to 100 minutes.