Document transforms/smoothing

[jkosciessa]

According to Elly Martin, the tissue transforms to the computational grid, and general smoothness of tissue transitions (while avoiding partial voluming of tissue properties) can impact simulation outcomes. We should document the decisions that occur in the pipeline.

I noticed that the alignment to the computational grid seems to occur via nearest neighbor interpolation in align_to_focus_axis_and_scale, something which Elly advised against.