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Investigating individual point defects, e.g. monovacancies, using TEM-related techniques was believed to be difficult because this requires both atomic sensitivity and atomic resolution and the specimens need to be very thin such that one can detect the individual point defects from the image contrast.

The experimental conditions of the microscope are also very important for point defect analyses, for instance, a probe current, applied in a JEM-2100F equipped with a delta corrector and cold field emission gun operated at 60 kV, to analyze monovacancy in single-layered h-BN (hexagonal boron-nitride) by STEM-EELS was approximately 40 pA.

It is difficult to get EELS energy resolution down to 200 meV or better.

In many cases, it is difficult to rule out thickness effects on the total signal, for instance, at grain boundaries and rough interfaces.