Different from an amorphous material, in a crystalline material, two main additionally effects affect the measured EELS intensity:
i) Diffraction effects;
ii) Electron channeling effects.
Similar to the diffraction contrast mechanism of TEM imaging, diffraction contrast has a substantial effect on the EELS intensity as well. Under strong diffraction conditions there is a significant loss of intensity so that any direct spatial interpretation from SIs (spectrum images) is almost impossible.
Diffraction effects can modulate the EELS intensity, resulting in overestimation of inelastic mean free path (IMFP, λ) of electrons by up to 25%.  Those effects can be minimized by selecting appropriate sample orientation.
To avoid strong diffraction effects, for instance, spectra for silicon (Si) crystals can be recorded with the electron beam slightly out of zone axes, e.g. tilt 6.7° away from the  and 2° from the  axis.
In a single crystal or polycrystalline material, it is also difficult to measure the TEM sample thickness using the concept of a mean free path since the intensity of each Bragg-diffracted spot depends on the crystal orientations and is not proportional to crystal thickness. However, each reflection is characterized by an extinction distance, and thus more variables besides thickness cause the EELS intensity change.
Precise correction for elemental quantification extracted from EELS maps in crystalline specimens is a difficult task because it is complicated by the existence of electron diffraction, and channeling and blocking effects; it would require:
i) Measurement of intensity in the diffraction plane;
ii) Knowledge of the crystal structure;
iii) Knowledge of the orientation of the crystals;
iv) Measurement of the specimen thickness.
In summary, some technique can be used to minimize the diffraction effects:
i) Rocking beam illumination can smooth out the strong diffraction contrast, 
ii) Record elemental maps under hollow cone illumination ,
iii) Use precession electron diffraction to record the spectrum,
iv) Use a large convergence angle.
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