Table 3. Cell and intracellular events that can occur within a simulation cycle.

Cell-Level Events	Map to Intracellular Events
Cell state (& color) changes	MCell point assignment*
Cell division	CellCycle updating at simulation cycle 1
Lumen creation	Cell initiates dying
Lumen merging through TJ reorganization	Death advances; cell TA decreases
Lumen expansion through TJ reorganization	Polarity counter (polarCounter) begins
Lumen expansion without TJ reorganization	Decrement cycleCounter
Isolated point engulfed*	Decrement polarCounter
Cell perimeter (but not TJs) changes	Decrement shiftCounter (TS ISMA only)
Dying complete: cell disappears	Compute matrix and lumen contact length, A, TA, & TP
Matrix removal	Compute G for a potential index change
Cells change shape

*This event exists only within the ISMA system and has no specific cystogenesis counterpart.

All cell events produce a visible change within the ISMA visualization. Events that map to intracellular events result in a change within a cell, but do not produce a visible change within the ISMA. Cell-level events map to equivalent events between in vitro MDCK cells, lumen, and matrix, while intracellular events map to events (less well understood) within in vitro MDCK cells.