Small invertebrates like this [tardigrade](https://i.imgur.com/635ZaGu.jpeg) seen under an optical microscope are mostly transparent.
What you refer to are images created with an electron microscope (using, well, electrons in a vacuum and not light), which only produce shades of grey and not colors.
But the result can of course be digitally colorized afterwards like this other [tardigrade](https://i.imgur.com/yssbCSy.jpeg).
> Can we just not see color past a certain scale?
In a way. With light you can only resolve details up to the light’s wavelength, i. e. ~ half a micrometer. Hence the use of electron microscopes to peer at smaller things.
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