The smallest imaging element on an imaging sensor is the pixel. Specifically, the light sensitive aperture of the pixel element. It collects electrons that have been kicked into its potential well by incident photons during the exposure time. It then provides the digitizing component of the imaging system with a packet of charge.
In a non-color imaging system, the resolving element of the system is equal to the pixel (not considering any optical system degradation). Note that an electron kicked into the well by a 550 nm photon looks no different to the digitizer than an electron kicked into the well by a 450 nm photon.
In digital RGB color camera systems, the color of the light is determined by sampling light intensity in three bands of the visible spectrum: red (~530 nm – 700 nm), green (~460 nm – 600 nm) and blue (~400 nm – 500 nm). The color RGB digital image then typically consists of an array of data with three values for each pixel location corresponding to the red, green and blue color intensities for that location. Two popular methods in common use are Single Shot Color Mosaic Sampling and Three Shot Color Sampling:
One method of color sampling is to apply a red, green, or blue color filter directly onto each pixel. The filters are most commonly applied in a repeating four-pixel element called a Bayer Filter Pattern (see Figure 1).

To create a color image, a single exposure is taken, resulting in a sampling of only one of the primary red, green or blue colors at each pixel location. The two un-sampled colors are then interpolated from adjacent pixels that have values for the color being calculated (note that the other colors do not contribute anything to the color being calculated).
To construct a color RGB image from this sampling method, 66% of the intensity values must be calculated. Also note that the resolving element is the 2 x 2 Bayer Filter Pattern that was used to sample the image. This means that an image captured by a 2048 x 2048 sensor actually has resolution of only 1024 x 1024. How does this happen? Envision that we create a perfectly small ray of red light that falls entirely onto one red pixel with no other light falling on the sensor. What will the image look like? First, the red pixel that the red ray fell onto, will very accurately record its intensity value, and now the eight adjacent pixels that had no red light falling onto them will each have a value of red light calculated for them due to the interpolation. The resulting image will actually represent the one pixel ray as being nine pixel rays. Now imagine if our red ray fell onto a blue or green pixel; the resulting image would show nothing!
Other artifacts also result from this sampling method. Thin white lines and extreme brightness transition edges in images can appear to have color stripes due to sampling and interpolation errors (see Figure 2).

Another method of color sampling is to position a color changing filter element
in front of the sensor, then sequentially capture a red, green, and blue image.
A third is to use three sensors (3-chip or 3-CCD), one for each of the three
primary colors. The three sets of image data are then combined pixel by pixel to provide RGB
sampled color at each pixel location (see Figure 3).

One drawback to the color changing filter element design is that if the image is changing with time, the sequential image capture will produce an image with red, green and blue ghosts of your subject as it moves across the scene. Another possible concern is image exposure and capture time. This method triples the time, so if it is an issue with a single shot, it will be more of an issue with the three shot method. Thus, the 3-CCD option provides the best solutions for such cases, however there are many fewer camera models which have this feature.

As with any situation, the appropriate solution depends on your needs. If you have moving samples or need high throughput, then 3-CCD or single shot color mosaic cameras would be most appropriate. If your sample is fixed and you have additional time, then you may benefit from the additional resolution from three shot color cameras.

