Automatic ROI drawing ( IAAutoROI )

Parameters:

Name	Short Name	Type	Description
Frame	frame	integer	From which frame to calculate ROIs. 0 uses projection
Projection type	type	string	Generates ROI from projection image if the frame number is 0
Max number	maxnumber	integer	Maximal number of ROIs to place.
Minimal intensity (percentiles)	minint	real	Selects only cells brighter than the minimal intensity given in percents of the intensities between 5 and 99 percentile.
Progressive tolerance	progressive	boolean	If Yes, tolerance is changed in order to provide ROI sized between the minimum and maximum size limits
Tolerance factor	tolerance	real	Pixels dimmer than (mean-tolerance*stdev) are outside of the boundary of the ROI. This is the starting value, if progressive.
Gamma	gamma	real	Gamma correction to be applied on the intensity values before ROI drawing (this does not affect actual image data).
Minimum size (pixels)	minpixelsize	integer	Minimum number of pixels in the ROI.
Maximum size (pixels)	maxpixelsize	integer	Maximum number of pixels in the ROI.
Start size (pixels)	startpixelsize	integer	The initial mean and stdev values are calculated from a "Start size" sized patch of pixels. A median filter with start window size is applied, so larger start size overlooks small objects.
Dilation size (pixels)	dilatesize	integer	The ROI is finally dilated, or set it zero to disable dilation.
Exclusion size (pixels)	excludesize	integer	No other ROIs will be drawn into exclusion size vicinity of a ROI.

Description:

Draws ROIs automatically by repeatedly applying the magic wand tool on the brightest objects.
Staring with the brightest pixel of the image, the magic wand tool is applied with a given tolerance. If progressive tolerance is set Yes, and the encircled area is smaller or larger than the minimum or maximum size constraints, the magic wand tool is reapplied with increased or decreased tolerance, respectively. Otherwise regions outside of size constraints are discarded. The final ROI is grown by the Dilation size, and no magic wand tool is reapplied in Exclusion size vicinity. ROI drawing is performed in a median filtered projection image, where the frame range and type of projection is set by the Frame and Projection type parameters, and the window size of the median filter is the start size. The magic wand tool is reapplied on the remaining brightest pixels of the image, until Max number of magic wand applications is reached, or the brightest pixel has a lower intensity than the percentile value set by the Minimal intensity parameter.