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 e