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Microscopy vs Flow Cytometry



Fluorescence Microscopy and Flow Cytometry, both are biological instruments which are capable of measuring the biophysical and biochemical properties of cells or particles which are under study. Both of them are capable of identifying types of cells present in a given sample. These two technologies are useful in variety of applications and they have widespread usage... But, These two differ in their applications and use. 
Fluorescence Microscopy
Flow Cytometry
Sample mounted on a glass slide.
Sample is allowed to pass through a liquid stream through a sensing area. (Single cell suspension).
Produces magnified images of the cells
Does not produce the images.
Whole Tissue section can be visualized and analyzed
Tissue must be disintegrated into single cell suspension. And each single cell is analyzed.
Detection through human eye and images can be produced on a computer screen
Detection is electronic mode.
Electronic Data.
Xenon or Mercury-Vapor Lamp are used as light sources.
Usually, Lasers are used as light sources or excitation sources.
Sample number of cells are analyzed.
10-100s of cells on a slide
High Throughput analysis.
1000s of cells per second.
Objective Interpretation
Subjective Interpretation
Slow Analysis Time and Less Sensitivity
High throughput and High Sensitivity
Qualitative Results
Quantitative Results


Note: Both systems use Dichroic Mirrors and Emission Filters.

Fluorescence Microscopy: Microscope was invented before flow cytometry, fluorescence microscopy is improved version of a light microscope, uses the lasers as excitation sources to excite the fluorescence present in the specimen under study. Fluorescence emitted from the cells or particles present in specimen produces a magnified image. Fluorescence Microscope is useful to study the specific cell characteristics. With the help of this, cells can be quantified and can be analyzed qualitatively. However, number of cells or types of cells are limited. 



Flow Cytometry: with the help of this technology, cells or particles present in a suspension can be quantified and analyzed and perform measurement for the characteristics such as relative cell size, granularity and quantification of DNA & RNA, fluorescence and intracellular proteins. Results obtained from the flow cytometer could be absolute or relative data. The technology has been widely used for the identification and characterization of cells, cell types, cell counting, and identifying various extra and intra cellular protein markers, identification and characterization of micro organisms. 

Fluorescene Microscopy vs Flow Cytometry: 
       Fluorescence Microscope and Flow Cytometer, both are capable of measuring the cellular components quantitatively. But, they differ in how many cells they can handle, locating the cellular components, volume of the cells, number of parameters and also sample preparation. 

Fluorescence Microscope can show how the cellular components are distributed inside the cell (clustered or uniformly). It can also show the area of the cell and its structure. It can quantify the cellular components for 10-100s of cells and one parameter at a time is used. This technology produces magnified images of the cells. Sample preparation involves the mounting the specific number of cells on a slide and observe under the microscope to produce a magnified image. One fluorescence parameter can be used simultaneously. Can not sort the cells. 

But, where as 

Flow cytometer can not show the distribution of cellular components within the cells, But it can measure the fluorescence tagged with those cellular components and measure them quantitatively. It can produce relative data of the cell size,  cell granularity and other properties such as fluorescence data. It can handle up to 1000s of cells per second. (There is no magnified image). Sample preparation involves the preparation of single cell suspension and maintaining these cells dispersed in the suspension. Up to 15-24 fluorescence parameters can be used simultaneously. Also, target cells can be sorted using the technique called fluorescence-activated cell sorting and sorted cells can be further used for downstream applications. 


"Flow Cytometer and Fluorescence Microscope achieve same goals. They have their own roles, benefits, advantages and applications. Due to these reasons, it makes them suitable for the different specific roles" 


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