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Glossary terms about Fluorescence

A form of photoluminescence which persists only for a short period of time (usually less than 100 nanoseconds) after the cessation of excitation.

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Collecting Z stacks
(As an aside, this data was derived by collecting the autofluorescence signal emitted predominantly by the chitin exoskeleton when excitated with 488nm (blue) laser light. 
Components of the confocal microscope
In fluorescence microscopy these are usually combined in a filter block as is illustrated below. 
Confocal microscopy
The fluorescence (or reflection) from this spot is imaged by the same objective and brought to a focus at the pinhole. 
Detection parameters
Using the lowest possible laser power for the shortest possible time will best preserve the fluorescence or biological activity in your samples. 
Fluorescence microscope
Fluorescence microscopy
Some cell components (such as chlorophyll and phenolic compounds) are inherently fluorescent (autofluorescence). 
Image acquisition (single scan)
There are two different ways of calculating resolution, according to whether the specimen is illuminated externally (Abbe calculation) or is effectively self luminous as in fluorescence microscopy (Rayleigh calculation). 
Light microscopy
If we want to add in components for fluorescence, polarization and so on we are in trouble. 
Objective lens - magnification versus resolution
Köehler illumination  
Practical image acquisition
Comparisons like this also allow a very objective means to evaluate labelling protocols when titrating antibodies. Many samples will show some level of autofluorescence
Scanning and resolution
As the light hits the specimen, fluorescence photons are emitted and some enter the objective lens. 
Sequential and simultaneous
When collecting fluorescence images it is essential to understand the characteristics of the fluorescent dyes one is using and the configuration of the lasers and filters in the confocal microscope. 
Transmitted light microscope
Köehler illumination  
Virtual light microscopy
Transmitted light microscope