The need to operate with low ion beam fluences implies the images obtained using ion microscope (IM) are often grainy and have poor visual quality compared to what can be obtained using e.g. confocal microscopy. This results from the Poissonian distribution of counts in pixels. Here we report work on some different approaches for objectively improving the visual quality of IM images. In this work we present (i) dramatic improvement in the visual image quality of off-axis and direct-scanning transmission ion microscopy (STIM) images by suppression of zero-pixels; (ii) denoising of PIXE images using wavelet filtering and (iii) use of the feature preserving characteristics of wavelet filtering for co-localisation of weak trace elements.