On the importance of color in mass spectrometry imaging

Abstract

Mass spectrometry imaging (MSI) data visualization relies on heatmaps to show the spatial distribution and measured abundances of molecules within a sample. Nonuniform color gradients such as jet are still commonly used to visualize MSI data, increasing the probability of data misinterpretation and false conclusions. Also, the use of nonuniform color gradients and the combination of hues used in common colormaps make it challenging for people with color vision deficiencies (CVDs) to visualize and accurately interpret data. Here we present best practices for choosing a colormap to accurately display MSI data, improve readability, and accommodate all CVDs. We also provide other resources on the misuse of color in the scientific field and resources on scientifically derived colormaps presented herein.

A Guide to MALDI Imaging Mass Spectrometry for Tissues

“…Also, generating heatmaps to illustrate the molecular alterations in these large data sets are very popular. For both instances, an appropriate colormap is essential for the accurate and precise display of the data, otherwise the quantitative value is very little and in addition, it can be very misleading . Both the style and the color are critical and can play a critical role on the perceived structure within the data .…”

“…For both instances, an appropriate colormap is essential for the accurate and precise display of the data, otherwise the quantitative value is very little and in addition, it can be very misleading. 162 Both the style and the color are critical and can play a critical role on the perceived structure within the data. 163 Visualization software typically include multiple color schemes and rely on the user to select the most appropriate.…”

SMART: A data reporting standard for mass spectrometry imaging

“…In addition to dimensional scale bars, each ion image should be coupled with heatmap scale bars in a linear, color vision deficiency (CVD)‐compliant color scheme. Although rainbow color maps (e.g., jet ) are esthetically pleasing and commonly used in MSI publications, these should be substituted for scientifically derived color maps (e.g., cividis , magma , inferno , and viridis ) to avoid data misinterpretation 29–31 . Additionally, we would suggest stating any accompanying normalization strategy and data post‐processing information with the ion image (e.g., Normalized to TIC) if applicable.…”

“…Although rainbow color maps (e.g., jet ) are esthetically pleasing and commonly used in MSI publications, these should be substituted for scientifically derived color maps (e.g., cividis , magma , inferno , and viridis ) to avoid data misinterpretation. 29 , 30 , 31 Additionally, we would suggest stating any accompanying normalization strategy and data post‐processing information with the ion image (e.g., Normalized to TIC) if applicable. Other data processing methods to report may include but are not limited to the minimum or maximum abundance threshold cutoff and hot spot removal percentage.…”

Single-Image Multi-Parametric Representation of Optical Properties through Encodings to the HSV Color Space

“…Given the intricate relationship between perception biases and data visualization, numerous studies have explored the impact of different colormaps on the visualization and representation of identical 2D data [9], the creation of task-customized colormaps [10][11][12][13], as well as the best way to build a color-based representation [14][15][16][17]. Conventional colormaps, featuring diverse spectral arrangements, have the potential to elicit varied perceptual responses due to the interplay of color and luminance gradients.…”