Because of electron beam damage, especially in the measurements with field emission guns, S/TEM microanalysis needs not only high count rate capability but also high collection efficiency of the X-rays in order to reduce the dose on the specimen in EDS measurements. However, in many cases, it is possible to obtain only a limited number of counts in a spectrum due to different reasons such as beam damage or specimen drift.

The EDS intensity or count rate depends on many factors, e.g. the specimen position in EM (electron microscope) column. If the optimized alignments of EM system and EDS system do not match each other, the EDS intensity may not be maximized at the optimized condition of the EMs, for instance, at the optimized SEM working distance. In this SEM case, the EDS count rate can reach a maximum by adjusting the working distance.

Spatial resolution can be improved by small probes and thin specimens while these conditions are exactly the opposite of those required to obtain high count rates.

However, the input count rate of EDS detector is normally selected so that the system deadtime is generally less than 30%-50% in order to minimize the effects of pulse pileup and peak distortion.