Atomic Force Microscopy
Uses a laser and a sharp tip to probe the surface of sample. This technique offers a fully three-dimensional view of the sample's surface, without requiring a coating that alters the sample (as with scanning electron microscopy). However, an atomic force microscope's maximum scanning area is much smaller than that of other instruments - micrometers versus millimeters.
Unlike fluorescence microscopy, in which the entire sample is flooded with light, confocal microscopy excites only a particular point and uses a pinhole to further reduce out-of-focus information. A confocal microscope scans a series of these points to produce a 2D or 3D image. Different types of confocal microscopes may be optimized for either improved resolution or speed.
Passes a wave of electrons through a sample at regular intervals, creating cross-sections that are then constructed into a 3D image. These slices are collected using a transmission electron microscope.
A sample is labeled with a fluorophore and then flooded with light of a particular wavelength. This light is absorbed by the fluorophores and emitted again as a different color. The light used for illumination is separated using a filter, leaving the excited fluorophores visible.
Similar to confocal and fluorescence microscopy, multiphoton microscopy relies on fluorescence excitation. However, multiphoton microscopy reduces the damage (photobleaching and phototoxicity) that occurs with other techniques. Thus it can be used for 3D imaging of thick and living samples.
Scanning Electron Microscopy
Images a sample's surface by scanning it with a high-energy electron beam. A large depth of field shows a great deal of texture detail, for an image that looks three-dimensional. Samples are generally coated with one of a handful of metals (often gold) before imaging; this improves signal and spatial resolution, and reduces image artifacts for non-conductive samples.
Many microscopy techniques require some type of specimen preparation - mounting, freezing, dyeing (fluorescence microscopy), coating (electron microscopy), slicing (transmission electron microscopy), or otherwise altering the sample.
Transmission Electron Microscopy
A transmission electron microscope transmits electrons through an ultrathin sample, producing an image from the interaction between the sample and the electrons passing through. TEM offers much higher resolution and finer detail than light microscopy, but can only use samples at most hundreds of nanometers thick.
Combines a fast-motion video camera with a light microscope to caputure small and rapidly moving cells and structures. These movies can be replayed as high-speed time-lapse or real-time videos.