By the nature of their operation, there are some additional effects which are peculiar to CCDs. The unique feature of CCDs is that they are used as shift registers to transfer the charge through the detectors themselves in the process of readout. The parallel transfer efficiency (transfer efficiency from one row to the next) must be extremely good in order not to lose any significant amount of charge over the large number of parallel transfers which must be performed (especially in larger devices). For example, a charge transfer efficiency (CTE) of 0.999 per transfer, which sounds good, will result in a loss of 64% of the signal over 1024 transfers, or 83% of the signal over 2048 transfers! For detectors of these sizes, CTE's of order 0.99999 or better are required. Fortunately, they are achievable, though not trivially so; many devices are rejected because of inadequate CTE.
Charge transfer problems can lead to a variety of effects which are often encountered by CCD users, especially those pushing for the most accurate photometry. An example of one such problem is known as deferred charge. This occurs because some CCDs transfer charge less efficiently at very low light levels. Essentially, this makes the detector non-linear at low light levels. Deferred charge can be corrected for if exposure levels are above the level where the nonlinearities are important. Alternatively, if low light levels are expected, detectors which exhibit this problem can be ``pre-flashed'' in which a background level of photons is put on the chip before the exposure is started; when one does this, however, one must pay the price of additional background noise.
The manufacture of CCDs, especially the low noise devices with high quantum efficiency which are needed by astronomers, is a complex procedure; only several manufacturers currently attempt this. The quality of a CCD is generally specified by its quantum efficiency (as a function of wavelength), its readout noise, and charge transfer efficiency (though there are other figures of merit as well).
CCDs can either be illuminated from the front side (where the electronics are implanted) or from the back side. To work efficiently when back-illuminated, the chips must be thinned by some process. Generally, thinned back-side illuminated chips have higher quantum efficiencies than front-side illuminated chips. However, the thinning process can be difficult, with a relatively high fraction of attempts at thinning ending in failure. Front-side illuminated chips not only have lower quantum efficiencies, but tend to have particularly poor blue response.
An additional way to improve blue (or any) response is to coat the chip either with some sort of anti-reflection coating to minimize reflective losses, or with some sort of lumogen which converts blue (or UV) photons to longer wavelengths where the chip is more sensitive.
The quantum efficiency is never totally uniform over the entire chip. Pixel-to-pixel variations in q.e. are typically a few percent. Over larger scales, q.e. variations can be larger; larger q.e. variations are often found in thinned chips because the thinning process may be non-uniform. The variations in q.e. across the chip, along with possible differences in illumination pattern across the chip, leads to the necessity of flat-fielding.
An additional consideration rarely considered is whether there are quantum efficiency variations within each pixel. In the limit where sources are very well sampled (i.e. cover many pixels), these are irrelevant, but they would lead to direct systematic photometric errors in the situation where sources are undersampled. Little is known about the possibility of such variations in different devices, but it is likely that they exist at some level.