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.
Theoretical study of EELS mostly considers both the incident and scattered electron waves are plane waves. However if the incident electron experiences strong channeling, then it is not necessary that the incident electron is a plane wave but may be approximately the same size as the outer atomic orbitals. 
Based on the theory of electron inelastic differential cross section, using an incident 100 keV electron wave, Kirkland Obtained the relationship between EELS partial L2,3 cross section and energy loss (in eV) for single atom Si (silicon) produced by electron channeling through a  Si specimen at different depths, indicating the variation of EELS intensity (see Figure 2801).
|Figure 2801. EELS channeling effect at depths of (a) 10 Å, (b) 100 Å, and (c) 200 Å. The detector collection angle was 20 mrad. Adapted from 
Minimizing the channelling effect (dechannelling) can be achieved by:
i) avoiding incident electron beam in crystalline orientations along major zone axes,
ii) using thin specimens,
iii) using convergent beams.
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.
 Earl J. Kirkland, Some effects of electron channeling on electron energy loss spectroscopy, Ultramicroscopy 102 (2005) 199–207.