Here is my problem: I am trying to work around D600 notorious oil spots by using a dust off ref photo. Simple: open RAW file in Capture NX2, load the ref photo and get the spots clean. Next, I want to further process this clean photo with other software, say Photoshop or Photomatrix. I open the “clean photo” and voila, magic, the spots are still there. Naturally, I tried to Save/Save As the NEF file after processing with Capture NX2 with the same result. Incidentally when I do a “Save As” all the options are inactive (grey out). So there is this bizarre dichotomy: the same file has no spots in Capture NX2 (or View NX2) and spots in Photoshop. Has anybody found a solution (assuming that there is another person who cares about it)? Of course, you can save the file in TIFF of JPEG but that is NOT the solution I am looking for. Many thanks!
Almost all RAW convertors save the adjustments you make to a file as a set of instructions in a form only the program you used to make the adjustments with can understand. They do it that way so that the original data from the RAW file is not destructively altered. In the case of Nikon, the demosaicing algorithms Nikon uses are proprietary. Other applications that can convert .nef files are reverse engineered using their own proprietary algorithms.
In general the things that are "baked in" when a RAW file is converted to TIFF or JPEG are things like: White Balance, Exposure, Contrast, and Highlight and Shadow curves. If you go ahead and do these basic adjustments before exporting a file as a 16-bit TIFF then you can apply different adjustments from other applications at that point in your workflow without sacrificing much, if any, quality compared to applying those tools to an unconverted RAW file. In the case of an image with a wide dynamic range that you want to work with in Photomatix, you can export separate dark, medium, and light versions of the same image as TIFF files and combine them in Photomatix just as you would a set of bracketed exposures.