The choice of colour scheme used to present data can have a dramatic effect on the perceived structure present within the data. This is of particular significance in mass spectrometry imaging (MSI), where ion images that provide 2D distributions of a wide range of analytes are used to draw conclusions about the observed system. Commonly employed colour schemes are generally suboptimal for providing an accurate representation of the maximum amount of data. Rainbow-based colour schemes are extremely popular within the community, but they introduce well-documented artefacts which can be actively misleading in the interpretation of the data. In this article, we consider the suitability of colour schemes and composite image formation found in MSI literature in the context of human colour perception. We also discuss recommendations of rules for colour scheme selection for ion composites and multivariate analysis techniques such as principal component analysis (PCA). Graphical Abstract a–t Visualisation of the same data (unnormalised m/z 826 from the cerebellum region of a mouse brain) using colour schemes found in the MSI literature. Intensity spans from 0 to 100 counts. a Grayscale, b red, c green, d blue, e green to white, f cyan to white, g blue to white, h red to white, i pink to white, j copper to white, k hot, l pink hot, m green to yellow, n cyan to magenta to yellow, o double scale (blue to green, red to yellow), p temperature-based, q–t rainbow-based