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In order to study the effect, if any, that amyloid may have on functional properties of dendrites, a comparison between populations is necessary. For this comparison, the first clear step is to define the different populations of dendrites.

In the curvature and width analysis the populations that are being analyzed are mainly dendrites that are either in or out of the plaque. In order to define with a certain degree of precision the "status" of dendrites, the analysis starts by viewing the area covered by the amyloid, as presented in the following picture.

Next, the edge of the plaque is traced and used as a mask when only the other two channels (tau and healthy dendrites) are used.

The tracing is then performed inside or outside of the edge traced from the plaque. In the following picture, a partial trace of the healthy dendrites inside the plaque is shown.