. Author manuscript; available in PMC: 2013 Jan 20.

Published in final edited form as: Cytometry A. 2012 May 30;81(8):704–717. doi: 10.1002/cyto.a.22073

Table 4.

Comparison of intensity-based analysis with number-based analysis

	INTENSITY-BASED ANALYSIS	NUMBER-BASED ANALYSIS
Quantification	Normally relative but reflects total amount.	Absolute but only for the number of puncta or granules.
Automation	Yes, after background subtraction.	Yes, particle analysis can be used.
Whole-cell analysis	Yes	Yes
Normalization factor	Protein	Protein
Dependency on background	Background subtraction is needed.	Not critical; background is used for determination of signal from noise.
Signal/noise ratio	Important for analysis	OK if granule can be distinguished.
Standardization of staining and FISH	Same procedure and parameters should be used.	Same procedure and parameters should be used.
Image acquisition	Same procedure and parameters should be used.	Variations allowed.
Image analysis	Same procedure and parameters should be used.	Variations allowed.