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Are electron photographs showing electrical charges? Do electrically charged parts show up more (darker in the photo) ?

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Yes, because the electrons interact mainly electromagnetically, all of their other interactions are negligible to that.

Electronmicroscope generate a 2D plot, essentially a matrix, mapping the picture we made. It depends on the imaging software, how it maps the values to greyscale colors.

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  • $\begingroup$ This is incorrect - at least so far as "yes , electrically charged parts show up more" $\endgroup$ – Carl Witthoft Jul 16 '18 at 18:06
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If you read the excellent discussions on the wikipedia page, you'll see that a transmission electron microscope works on the same principle as an x-ray machine: the image shows how many particles/photons made it through the subject.

Other techniques analyze the various secondary products produced by electron collisions with the subject, such as heat or X-ray emission.

The charge or lack thereof on the subject material has essentially zero bearing on the final image.

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