DCFDA normalized rate in all cells of a whole view field

Parameters:

Name	#	Type	Description
Background Level (percentile)	1	real	Background is calculated as frame-by-frame mean of those pixels that are the darker than this percentile of image histogram for the duration of the entire recording.
Mask sensitivity (0.2-1.5)	2	real	Sensitivity factor, typically 0.2-1.5
Range for rate measurement	3	string	The range of the first part of the experiment where the rate is to be measured, in frame numbers
Place positions into columns	4	boolean	Data from multiple stage positions will appear in new columns instead of being appended below the existing data. This option requires the MD output to be turned on.

Description:

This pipeline calculates the rate of increase in fluorescence intensity in a single channel, normalized to percents of the difference between the baseline and the endpoint. The typical use is measurement of H2O2 production using DCFDA-AM.

Experimental paradigm: the time lapse consists of two parts, recording of a rate (e.g. 10-15 frames of time lapse capturing increasing fluorescence), then adding saturating amounts of H2O2 and recording of a plateau. The rate will be calculated as %/sec of the full oxidation. The normalization is calculated based on the first n and last n frames where n is set in the Preferences/Misc/Normalization and DF/F0 panel. Background is subtracted, and cell-free areas, determined in a maximum intensity projection image are masked. The output is based on the mean fluorescence intensity of all cells in the view field.

Version history:
2: typo fixed