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et al. (1981a). The variance is a function that is spatially varying, for two reasons: (i) the noise statistics varies with the electron dose, which in turn is proportional to the local image intensity, and (ii) part of the observed variations are "signal associated"; that is, they arise from components of the structure that differ from one particle to the other in density or precise location. Usually, no statistical models exist for these variations.

The variance map is particularly informative with regard to the signal-associated components as it allows regions of local inconsistency to be spotted. For instance, if half of a set of molecules were carrying a ligand, and the other half not, then a region of strong inconsistency would show up in the variance map precisely at the place of the ligand.

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