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The D800E differs from the D800 by incorporating optical glass between its OLPF substrates that eliminates the blurring effect of the OLPF. This optical glass reorganizes the path of light reaching the sensor and essentially un-polarizes it, causing it to strike the sensor in a straight path. By eliminating this effect and straightening the path of the light, images are recorded with higher sharpness and resolution.
The idea of increased sharpness and resolution sounds like an ideal consequence, but the risk of spatial aliasing, moiré and color shifting is certainly increased. The D800E does not provide an in-camera solution for anti-aliasing, so it is specifically designed for photographers who can effectively control their lighting situations and are more apt to spend time correcting images during post processing. The benefits of the D800E are also most noticeable when working with the RAW (NEF) file format.
When photographing in JPG or TIFF formats with the D800E, in-camera image processing dramatically reduces the efficacy of any subsequent alteration of moiré patterns in post production. Because of this automatic image processing, moiré patterns are essentially fixed into the file and dramatic pixel manipulation will be required to remove them during post production. By contrast, with the D800, your workflow can be the same whether you’re recording RAW (NEF) or JPG or TIFF files.
It should also be mentioned that while the moiré patterns will be more prevalent in images captured with the D800E, image processing tools such as Nikon’s Capture NX 2 and Adobe Lightroom 4 now feature plug-ins to simplify the removal of aliasing. This addition to your workflow could prove to be quite a chore when bulk-editing files, but these tools are promising solutions for moiré elimination.
Some points to take away when considering which model is most appropriate for you:
Both cameras feature an optical low-pass filter (OLPF); however, only the D800 truly makes use of it to reduce aliasing, moiré and false color.
The D800E incorporates an optical glass element between the substrates of the OLPF that negates their effect and results in greater sharpness and resolution in imagery. This increase in definition comes at the expense of an increased likelihood that moiré patterns and false colors will occur.
The D800E is an ideal camera for photographers who can very precisely control their shooting situations (i.e. studio and commercial setups). This involves control over the lighting, a steady camera (often with the use of a tripod), the ability and desire to photograph with middle f/stops (roughly f/5.6 to f/11), photographing only in RAW (NEF) file formats and a post-processing workflow that allows for the removal of moiré and false colors.
The D800 is an ideal camera for all shooting situations and allows you to work in any file format. There is no compensation required to reduce moiré.
With this difference aside, it should be noted that both cameras are highly capable of recording outstanding imagery. While the D800E could be perceived to be the better camera, this is certainly not true for everyone. You should make a careful consideration of your personal needs and shooting styles before determining the best model for you.