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The fill factor of an 
image sensor An image sensor or imager is a sensor that detects and conveys information used to form an image. It does so by converting the variable attenuation of light waves (as they refraction, pass through or reflection (physics), reflect off objects) into s ...
array is the ratio of a pixel's light sensitive area to its total area.
For pixels without microlenses, the fill factor is the ratio of photodiode
A photodiode is a semiconductor diode sensitive to photon radiation, such as visible light, infrared or ultraviolet radiation, X-rays and gamma rays. It produces an electrical current when it absorbs photons. This can be used for detection and me ...
area to total pixel area,
but the use of microlenses increases the ''effective fill factor'', often to nearly 100%, by converging light from the whole pixel area into the photodiode.
Another case that reduces the fill factor of an image is to add additional memory beside each pixel, so as to achieve a global shutter on CMOS sensors.
References
Image sensors Ratios {{tech-stub