There are at least two types of microscope that can give 3D images. Confocal microscopes that use lasers to illuminate the object and scanning electron microcopes (SEM) that use an electron beam. A SEM can give better magnification than confocal but confocal can image live moving subjects. In SEM the object of intrest must be coated with gold so only dead things can be imaged.
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The position of an image under a microscope varies based on the type of microscope being used. In a compound microscope, the image is formed inverted and reversed from the object being observed. In a stereo microscope, the image is typically upright and not inverted.
Actually, the image doesn't form in the microscope. The image forms on your retinas. The microscope focuses light in such a way that it comes together correctly on your retinas.
A transmission electron microscope (TEM) directs a beam of electrons through a thin specimen, producing a transmission image. A scanning electron microscope (SEM) scans a focused beam of electrons across the surface of a specimen, producing a 3D-like surface image based on electron interactions.
The objective lens is responsible for producing a magnified image on the inside of the microscope. This image is then further magnified by the eyepiece lens before it reaches the eyes of the person using the microscope.
The principle of image formation in a compound microscope states that the second lens magnifies the image formed by the first lens. The use of two lenses enhances the magnification of the image.