This transmission EM picture shows mitochondria clearly. They have the classic appearance of double walled oval structures, with internal cristae for the amplification of surface area. (The long snake-like structures in among them are invaginations of the plasma membrane.) The cytoplasmic matrix is significantly denser than the cytoplasm of the cell, and the dark dots inside the mitochondria are mitochondrial granules, condensations of calcium ions that are fairly commonly seen. The activity of mitochondria is dependent at least in part on ion flux and the movement of charged particles across the inner and outer membranes.
Mitochondria are a very nice example of a structure whose true nature was appreciated only after the introduction of the electron microscope. They were know to exist as early as 1890, because with special stains they can be seen with a light microscope. They're so small, however (about the size of bacteria) that in an LM they appear as little more than dark dots. By the 1920's and 1930's it was clear what their function was, but they remained a "black box" which consumed oxygen and produced ATP. The development of the EM, with its high magnification and high resolution, made it possible to look inside the box, to see how it was built, and to formulate testable hypotheses about how it functioned. As with so many other aspects of the life sciences, the current picture of the mitochondrion and its function is built on fundamental observations made with the electron microscope.
Mitochondria were discovered in the 19th Century and by the mid-1920's there was consensus on what they did: took in oxygen and put out ATP. But they were a "black box." No one had a clue how they did it. It wasn't until the use of the transmission EM that it was possible to look inside them, see how they were made, and begin to formulate hypotheses as to how they worked. The TEM revolutionized the life sciences: it created a whole new discipline, cell biology. Today, everything students are taught about cells, cell physiology, histology, and tissue architecture--all of it, including genetic engineering--rests on the foundation laid by the early electron microscopists of the 1940's and 1950's.
Amphiuma kidney, Janus Green stain, paraffin section, 400x