tl;dr: Many scientific journals take a heavy hand when it comes to color choice in illustrations, with the noble goal of aiding colorblind readers. I argue that this policy is outdated, and in fact hurts the community it is intended to serve.
For example, the journal eLife (full disclosure: I contribute free services to this journal) instructs its authors: “When preparing figures, we recommend that authors follow the principles of Colour Universal Design (Masataka Okabe and Kei Ito, J*FLY), whereby colour schemes are chosen to ensure maximum accessibility for all types of colour vision.”
This policy has been superseded by the fact that everyone reads eLife on a computer display of some kind. And by now all computers offer a customized color transform for color-blind people. See these links for Windows, MacOS, and iOS. These color filters replace whatever colors are on the display with new colors that are best discriminated by someone with a color vision deficiency. Most importantly the filter can be optimized for the user’s specific form of color blindness. This service has been wildly popular with colorblind readers.
Under these conditions, following the eLife policy is in fact detrimental to colorblind readers. Recall that there is no single color palette that works best for all forms of color blindness. If the author adapts the palette to a particular 2-dimensional color space, say protanopia, that will be suboptimal for other readers. Here is an example using the document that the eLife policy cites for guidance (Okabe and Ito).
“Original” shows a classic red-green fluorescence micrograph. Below that is the color substitution recommended by Okabe & Ito: turn red into magenta. To the right are 3 images produced by the Mac OS filters for different forms of color-blindness (I photographed my display with my phone – crazy, I know). The version that Mac OS produces for protanopia is very close to what Okabe and Ito recommend. But note the other two versions for deuteranopia and tritanopia are quite different.
So following the recommended policy will favor protanopes but hinder deuteranopes. What is more, adapting the color palette to one of these abnormal color spaces will make it more difficult for the operating system to optimize the display for another space.
In conclusion the best policy for authors is to do what comes natural: choose colors that use the widest color gamut possible. Then let the user’s display device take over and implement that specific user’s preferences. By analogy, we don’t ask authors to write with 36-point font because some readers have poor vision. We know that the reader can turn up the magnification as suits her preference. The same is now true in color space.
Bits, Brains, and Behavior 
Interesting point of view. And ut makes sense to me (as a color-blind person). A problem however still remains when figures from papers are used for in-person lectures (research talks or academic teaching). I have vivid memories of biochemistry lectures ten years ago where protein structures in green and red had been copied from papers of the 2000s, and I could not see anything in this mess. Sometimes, you cannot avoid losing visually handicapped people. But if a figure uses only two colors which don’t segregate spatially, thinking twice does not cost too much, in my opinion.
In the picture above, red and green are actually not so difficult to distinguish since green is distributed in a more blurry way. Most color-blind people are very good at using these kind of structures to infer color.
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Interesting points! A point of clarification re the final recommendation to “do what comes natural: choose colors that use the widest color gamut possible.” By most (trichromat-calibrated) perceptual metrics, green is – if anything – a bit closer to red than to magenta. Are you therefore recommending that folks should continue using magenta instead of red, at least in the common use case of two-channel microscopy images?
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