For SEM images it is acceptable to change brightness, contrast, levels (as in Photoshop) when these manipulations are applied to the whole image. All other manipulations are unacceptable without disclosure and anyway they seldom give good results.
Firstly, you can modify the brightness, contrast etc of SEM images, and EDAX spectraby either using some image editing software or by the instruments inbuilt softwares. Secondly, XRD and TGA data, you could use origin, tecplot etc graph plotting softwares.