Nikon D800E has a
36.0MP Full frame (35.9 x 24 mm ) sized CMOS sensor and features Expeed 3 processor. On the other hand, Canon 90D has a
33.0MP APS-C (22.3 x 14.9 mm ) sized CMOS sensor and features DIGIC 8 processor.
Another difference between these two cameras is that Nikon D800E's sensor lacks anti-alias (Low-Pass) filter. Removing anti-alias filter increases the sharpness and level of detail but at the same time, it increases the chance of moiré occurring in certain scenes.
Below you can see the D800E and 90D sensor size comparison.
As seen above, Nikon D800E has a 2.6x Larger sensor area than Canon 90D. Larger sensors give photographer more control on the depth of field and blurry background compared to smaller sensor when shot in same focal length and aperture.