Specimen preparation
Given the size of the surviving specimens, to say nothing of the tiny size of the microscopes, Leeuwenhoek looked at bits of things: plant parts, pond water, and animals' internal organs. If they couldn't be impaled on the pin behind his lens, he stuck them there with spit or glue.
Other things, he would let dry or leave damp on a bit of glass, and then glue the glass to the pin.
These specimens were dead. But the smaller specimens, the animalcules that we now call protozoa and bacteria, were living and moving and reproducing and dying. Leeuwenhoek not only had to make them visible, he had to keep them visible long enough to observe their life cycles.
The smallest sort of which I shall here speak, I see alive and exhibit as plainly to my eye as one sees, with the naked eye, little flies or gnats sporting in the air, though they may be more than a hundred million times less than a coarse grain of sand; for not only do I observe their progression, both when they hurry, and when they slow down, but I see them turn about, and stand still, and in the end even die.
Some of Leeuwenhoek's specimens were transparent or thin enough to pass or transmit light through them. They either came that way or he sliced a thin-enough section. The section that survives and Brian Ford, who examined it, described it as "sliced with a razor" to .2 mm thick, good even by today's standards.
For everything else, Leeuwenhoek relied on light reflected off the specimen. Many of his specimens were living, moving creatures. Others were anatomical structures whose three-dimensionality would be destroyed by slicing into sections.
Late in his career, Leeuwenhoek had some muscle tissue that he wanted to see better. He stained it with saffron, and was able to see details that he could not see before, but this does not seem to be a technique that he used before or after.