Why tissues are stained

Before a tissue can be seen under the microscope, it is cut into very thin slices and stained, that is, given color. Each dye sticks to a different part of the cell, and that is how it brings out what you want to see.

Hematoxylin and eosin are used together. The first one, hematoxylin, is a basic dye, and by simple chemistry it sticks to the acidic structures of the cell, which is why those are called basophilic. Whatever it grabs turns violet blue.

In practice that colors the nucleus, home of the DNA that is the cell's instruction manual, and also the rough endoplasmic reticulum, the protein factory. The second dye, eosin, is acidic and does the opposite: it turns the cytoplasm, the material that surrounds the nucleus, pink. Hence the classic slide, with blue nuclei against a pink background.

There are also special stains, aimed at a single target. They are excellent at their job, but they come at a cost: while they mark that target, the rest drops out of view. That is why several slides are usually prepared from the same sample, each one stained a different way.