Analytical and Bioanalytical Chemistry

, Volume 407, Issue 8, pp 2047–2054 | Cite as

Optimisation of colour schemes to accurately display mass spectrometry imaging data based on human colour perception

  • Alan M. Race
  • Josephine Bunch
Part of the following topical collections:
  1. Mass Spectrometry Imaging


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

at 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


Mass spectrometry imaging Colour scheme Data visualisation 



The authors wish to thank Andrew D. Palmer, Rory T. Steven and Rian L. Griffiths for helpful discussions relating to this work. Funded by EPSRC grant EP/F50053X/1.

Supplementary material

216_2014_8404_MOESM1_ESM.pdf (5 mb)
ESM 1 (PDF 4.95 MB)


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Copyright information

© Crown Copyright 2015

Authors and Affiliations

  1. 1.School of ChemistryUniversity of BirminghamBirminghamUK
  2. 2.Surface and NanoanalysisNational Physical LaboratoryTeddingtonUK
  3. 3.Surface and NanoanalysisNational Physical LaboratoryTeddingtonUK
  4. 4.School of PharmacyUniversity of NottinghamNottinghamUK

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