Imaging Resource publishes a very nice article "Pixels for Geeks: A peek inside Nikon’s super-secret sensor design lab" by Dave Etchells. There is quite a lot on Nikon-internal stuff that has been publicly released for the first time. Just a few interesting quotes out of many:
"Nikon actually designs their own sensors, to a fairly minute level of detail. I think this is almost unknown in the photo community; most people just assume that “design” in Nikon’s case simply consists of ordering-up different combinations of specs from sensor manufacturers.
In actuality, they have a full staff of sensor engineers who design cutting-edge sensors like those in the D5 and D850 from the ground up, optimizing their designs to work optimally with NIKKOR lenses and Nikon's EXPEED image-processor architecture.
As part of matching their sensors to NIKKOR optics, Nikon’s sensor designers pay a lot of attention to the microlenses and the structures between them and the silicon surface. Like essentially all camera sensors today, Nikon’s microlenses are offset a variable amount relative to the pixels beneath, to compensate for light rays arriving at oblique angles near the edges of the array."
Apparently, Nikon uses Silvaco tools for pixel device and process simulations:
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