The objective of our work is to develop a tool for automatic analysis of 2D membrane protein crystal images
in Transmission Electron Microscopy (TEM). The success of crystallization experiments is evaluated at high
magnification. The crystalline structure of a membrane can be observed when no other membranes are superposed.
It is therefore necessary to identify mono-layer membranes. In this paper we introduce an algorithm
that determines the stacking-level of membranes. Our method determines a quantum, a gray-level quantity that
is characteristic of a non-stacked membrane. In this way we are able to label each region qualitatively and
construct a stacking-level map that distinguishes from non-stacked to up to four-level stacked membranes. This
map provides the regions that will trigger a new image acquisition at higher magnification.