Rescaling image intensity with reference image choice

Parameters:

Name	#	Type	Description
Reference image operation	1	string	Use a positive control as reference image, where are many cells (objects of interests) or high fluorescence intensity. Using a positive control avoids amplifying background noise in wells with little or no detail.
Debris cutoff (top percentile)	2	real	This percentile of the image histogram sets the intensity value where the maximum of the Look Up Table (LUT) is scaled. Use -1 to override this with fixed value set below at "Max value".

Description:

This snippet rescales images intensities to a range 0-100. The 100 value is either taken at the given percentile of the actual image, or at the same percentile of a reference image. The snippet can also create the reference image.

Reference image operation: When “Reference image operation” = ”Self-referenced” image scaling is independently calculated for each image. This works well if none of the samples have very few, e.g. <5% of positive cells. If cell density or marker positivity greatly varies between samples, or if some samples have very few cells or few positive cells, use positive control reference. The positive control is one of the images from the data set with about maximum number of cells and positive cells. To make reference image set “Reference image operation” = ”Make reference image”. Process a positive control sample. The reference images will be minimized, and reused at the following operations. Then set “Reference image operation” = ”Use reference image” and process all data. To process a different data set, make new reference images. Old reference images areautomatically closed.

Version history:
V2: Added hint