A regular biological microscope shines the light from below. This is good for looking at cells, but not so useful when looking at something opaque. A metallurgical microscope shines light from above, through the lens. They are used for examining metal samples, rocks, and other opaque things.

An external light works for something like an inspection microscope. But as you increase the magnification, you need something like a metallurgical microscope that focuses the light where you are looking. Otherwise, the image gets dimmer and dimmer as you zoom in.

In some places, you've shown the same part of the circuit both with and without the metal layers. How did you find the same location on the die after taking the die out of the microscope, removing the additional layers and putting it back?

I figured that I would want to study the standard-cell circuits, so I made a detailed panorama of one column of standard-cell circuits with the metal. Then after removing the metal, I made a second panorama of the same column. This made it easy to flip back and forth. (Of course, it would be nice to have a detailed panorama of the entire chip, but it would take way too long.)

Biological microscopes illuminate the sample from below, as the samples are typically transparent. Metallurgical microscopes illuminate reflective samples from above.

*"Below" meaning "on the opposite side from the objective" - you illuminate _through_ the sample.

Metallurgical microscopes illuminate the sample "from the top side". The actual implementation even goes as far as making sure the illumination happens on the optical axis of the objective (as if the light was emitted from your eyes/camera, reflected from the sample and then seen by your eyes/camera). They are also called reflected light or epi-illumination microscopes.

Biological microscopes, on the other hand illuminate the sample from the back side (which doesn't work for fully opaque objects).