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Using The GIMP (or Photoshop) to Improve Photos?
Nom du Keyboard asks: "Is it possible to use The GIMP (or Photoshop) to improve my digital photos? I have a mid-range 7.1MP Olympus camera capable of shooting in Raw mode. When I inspected a section of clear blue sky on a bright, sunny day (which I've long believed to be relatively good reference of uniform color and brightness) I was surprised (disappointed, since I expect digital perfection) at the variance in adjacent pixels. It's also a quick way to identify any bad pixels. Surprisingly, actual photos from this camera look pretty good despite this variance so far. Moving on from that point it led me to wonder that, if you shot a uniform white surface, perhaps blurred as much as possible to avoid any imperfections in the surface itself, could a correction (adjustment) layer be created in GIMP or Photoshop exactly tuned to your camera that fixed the variations in your CCD sensor and improved the image quality in the process. Any thoughts?"
Yes, your $1000 digital camera is not going to have a perfect CCD. There is no such thing as a perfect CCD. And I don't understand why you care unless you're trying to do science work with it. Look at it this way, no one is ever going to look at your picture and say its horrible because one pixel is slightly different than the one next to it. You look at the content of the whole photograph, not three pixels.
If you are trying to do science, then a DSLR is not what you need. DSLRs use Bayer interpolation to create a color image. This inherently kills your accuracy since not every pixel in the image is actually a pixel on the camera. CCDs used for astronomy (which cost more than your whole camera) do not do this and they still suffer from the effects you mentioned. Every exposure used for scientific work goes through a whole data reduction process that tries to remove as much noise as possible. Others have mentioned most of the process (bias frames, dark frames, and flat fields), but most astronomical CCDs also have an overscan region which is part of the CCD that is not exposed to light and is used to record the thermal noise on the CCD. This changes from exposure to exposure and from temperature to temperature (and yes I am a researcher in astronomy).
In short, there's no reason for you to care about this, and there's no chance of fixing this completely (CCDs are not digital - they're analog). There's also no way of applying the same solution to every photograph (and CCDs can change over time). Don't worry about pixel-to-pixel variations and just take photographs for their content. If you're really interested in how CCDs work, read the Handbook of CCD Astronomy by Steve Howell. Its a great introduction to CCDs and how to use them for astronomy.