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.  Such channelling effect can strongly reduce the EELS
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 2801a).
|Figure 2801a. 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.
Estrade et al. employed precession electron diffraction technique on EELS measurements and observed that the channeling effect is reduced with precession-on and thus the EELS signal is enhanced at non-zero angles and suturated at a precession angle of 0.5° (~9 mrad)
as shown in Figure 2801b even though the TEM sample is aligned along a zone axis. The TEM sample thickness was 30 nm. This is reasonable because the electron beam is not really at the zone axis of the crystal of the TEM sample even though the optical axis is along the zone axis.
|Figure 2801b. EELS Signal Enhancement (SE) as a function of precession angle for the SiL2,3 edge in
a Si crystal in  zone axis conditions. SE = (I(α)-I(0))/I(0),
where I(0) stands for the intensity obtained without precession and I(α) for precession-on at the precession angle α. 
 Earl J. Kirkland, Some effects of electron channeling on electron energy loss spectroscopy, Ultramicroscopy 102 (2005) 199–207.
 Sonia Estrade, Joaquim Portillo, Lluıs Yedra, Jose Manuel Rebled, Francesca Peiro, EELS signal enhancement by means of beam precession in the TEM, Ultramicroscopy 116 (2012) 135–137.