Most microscopes that you see in a typical laboratory environment are compound microscopes. They are designed with objectives on a rotating nosepiece mounted above the stage, and the light source and condenser below the stage. They are most commonly used for viewing samples that have been fixed to a flat slide.

In certain applications it is necessary to look at live, unfixed samples. A more practical microscope design to use is the inverted microscope. An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. Inverted microscopes are useful for observing living cells, tissues or organisms at the bottom of a large container (such as a tissue culture flask). This allows you to examine the specimen under more natural conditions than on a glass slide, as is the case with a conventional compound microscope. You can place a Petri dish or other container on the stage and view the samples from below, thus not disturbing their more "natural" states. Larger, covered samples are less susceptible to evaporation and increases in temperature, thus preserving suitable living conditions for the specimen you are viewing.

Because of the fact that you have to look through thicker containers you often find the objectives to be long working distance or ultra-long working distance. These objectives have been corrected for observing samples that are further away than what you normally see on a compound microscope. The image may not be quite as clear as when you are looking at a perfectly flat slide. You may want to use a plastic Petri dish rather than a glass one as the plastic dishes are thinner and more uniform. Most inverted microscopes will have objectives that range from 4-40X, with 60X being an added option. You do not usually find inverted microscopes that incorporate 100X objectives.

Inverted microscopes can be configured for work in electrophysiology, in vitro fertilization, micromanipulation, high-resolution DIC, video-enhanced observations, and a variety of advanced fluorescence techniques. Motorized accessories can include shutters, filter wheels, revolving nosepieces, fluorescence block turrets, focus drives, and condensers. Inverted microscopes also allow you to add advanced objectives for water immersion, ultraviolet excitation, and phase contrast. Prices for inverted scopes vary according to the number and types of accessories you add to them, just as in compound microscopes.

The fundamental advantage of an inverted microscope is that it allows you to accept a container with a large and relatively long-lived diverse culture of live organisms without any preparation. This can be invaluable to work which requires the sample to be alive and in as natural an environment as possible.