Dear Vladimir. I would say, it depends almost entirely on your sample and the question of what you want to do with it. The classical microscope is upright, with the objective coming from above the sample (usually a glass slide with coverslip). However, if you want to observe a water filled petri dish through a glass bottom, then an inversted stand is obviously the system of choice. In the real world, most experiments can probably be done with both kinds of stands. However, the inverted microscope leaves you more space to operate above the plane of focus (which you observe) and thus, more and more systems are now configured in the inverted orientation.

Recently, Lightsheet microscopy is attracting more and more users. This is a totally different setup, where the objective is looking from the side and the sample is hanging from above or standing from below.

http://www.zeiss.com/microscopy/en_de/products/imaging-systems/lightsheet-z-1.html#introduction

So everything is possible. It depends on what exactly you want to do ...

http://www.zeiss.com/microscopy/en_de/products/imaging-systems/lightsheet-z-1.html#introduction

Dear Vladimir. I would say, it depends almost entirely on your sample and the question of what you want to do with it. The classical microscope is upright, with the objective coming from above the sample (usually a glass slide with coverslip). However, if you want to observe a water filled petri dish through a glass bottom, then an inversted stand is obviously the system of choice. In the real world, most experiments can probably be done with both kinds of stands. However, the inverted microscope leaves you more space to operate above the plane of focus (which you observe) and thus, more and more systems are now configured in the inverted orientation.

Recently, Lightsheet microscopy is attracting more and more users. This is a totally different setup, where the objective is looking from the side and the sample is hanging from above or standing from below.

http://www.zeiss.com/microscopy/en_de/products/imaging-systems/lightsheet-z-1.html#introduction

So everything is possible. It depends on what exactly you want to do ...

http://www.zeiss.com/microscopy/en_de/products/imaging-systems/lightsheet-z-1.html#introduction

Dear Vladimir.

Inverted microscopes are especially useful to examine the (polished) surface of heavy and large sized workpieces for industrial purposes. The inverted metallurgical microscope for example provides a very stable microscope table and unlimited open space, compared to a normal upright microscope, that has very limited distance between the relatively weak table and the objective.

I highly recommend you to take a look at the Olympus Microscopy Resource Center:

http://www.olympusmicro.com/index.html

and the similar site from Nikon

http://www.microscopyu.com/articles/formulas/

that will help you with your questions. Both have extensive coverage of basic and advanced topics.

Particular links to the inverted microscope design:

http://www.olympusmicro.com/primer/techniques/fluorescence/anatomy/fluoromicroanatomy.html

http://www.olympusmicro.com/primer/techniques/fluorescence/tirf/tirfconfiguration.html

http://www.olympusmicro.com/primer/java/tirf/prism/index.html