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In the dpreview.com discussion thread, DX mode on the D850, a user states that:

Second the smaller the sensor size the lower the signal / noise is. Using the camera [Nikon D850] in dx mode means giving up on the better high iso performance of an Fx camera compared to a dx camera. The D850 for instance in mode performs at D500 levels (give or take some small difference of no practical relevance).

This sounds to me that the low light performance decreases when using the camera in crop mode. Of course noise will be more visible if the cropped picture gets blown up to the same size because it has less resolution.

Is there any difference in performance/image quality by setting the camera to crop mode rather than cropping later to the same size? (Ignoring the fact that cropping later gives much more flexibility in composition - just talking about image quality and performance).

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No, there is no difference between crop mode or cropping in post.

Pretty much every image characteristic comes down to light per area. If you record the subject the same size (with the same exposure settings) on a larger sensor, it is recorded physically larger. So you get more area of the same light (larger area/same density). And when output at the same display size that becomes more light w/in the same area (same area/greater density)... i.e. more light/area.

The crop/smaller format will show more noise at any given display size simply because it contains less light, and the displayed image has less light density per image area.

In fact, there's no real/significant difference compared to using a TC or a variable aperture zoom lens instead either... although variable aperture zoom lenses don't typically loose light at a linear 1:1 rate.

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No difference in image quality at the pixel level. The better lowlight performance of a fullframe camera is due to having a larger image circle that is, at equal equivalent focal length (and thus equal framing) filled from the light of a larger entrance pupil. Better noise performance at the pixel level only results if you actually use that larger image circle for filling larger pixels.

A 50MP full frame camera has similar noise performance per pixel as a 20MP DX camera. If you are not pixel-peeping and have a display device with lower resolution than the camera, with more pixels noise will average out better. How much so depends on the interpolation the device uses. Nearest neighbor interpolation does not average noise at all, box car interpolation averages noise maximally but is rarely used because of its weak Moiré pattern performance.

However, you are talking about using an FX capable system in DX mode. This does not waste light over cropping the end result (such as when using a prime lens and not being able to move closer) but it does waste light over just zooming in and using the full sensor, then downscaling from that. So if you have the ability to zoom in, either because your lens is not at full zoom or because you can "zoom with your feet", that tends to make better use of your equipment regarding the light gathering capability. Of course at the cost of a reduced depth of field. If you'd have to stop down the lens in full-frame mode, you'd not work with more light anyway.

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