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Image manipulation tasks fall into several categories. You might want to fine-tune your images, retouch them, change color balance, composite several images together, and perform other tasks we know as image editing, with a program like Adobe Photoshop, Photoshop Elements, or Corel Photo Paint.
You might want to play with the settings in RAW files, too, as you import them from their .arw state into an image editor. There are specialized tools expressly for tweaking RAW files, ranging from Sony’s own Digital Image Converter to Adobe Camera Raw, and PhaseOne’s Capture One 5 Pro (C1 Pro). A third type of manipulation is the specialized task of noise reduction, which can be performed within Photoshop, Adobe Camera Raw, or tools like Bibble Professional. There are also specialized tools just for noise reduction, such as Noise Ninja (also included with Bibble) and Neat Image.