public class RATS_
extends Object
implements ij.plugin.filter.PlugInFilter

RATS_ (Robust Automatic Threshold Selection) ImageJ plugin. For use with companion RATSQuadtree class. Adaptation of C implementation by M.H.F. Wilkinson, 2000. Based upon work of M.H.F. Wilkinson and others, RATS establishes regionalized thresholds for a greyscale image where the regions are established using quadtree architecture. Within each of the lowest quadtree regions the threshold is calculated as the sum of the orginal pixels weighted by the gradient pixels. threshold = SUM(edge*orig)/SUM(edge) for pixels within each region. The threshold calculated in each region is required to meet minimum criteria - these criteria are determined by the user as a noise estimate (sigma) and a scaling factor (lambda). The user may also select the minimum region size. The thresholds for all region are then interpolated (bilinear) across the entire image. In general, the best values for each of three parameters are determined by trial and error for a given suite of images. Plugin Author: Ben Tupper (btupper@bigelow.org) for Mike Sieracki at Bigelow Laboratory for Ocean Science. Plugin Version: 2009-01-08 2009-12-11 BTT small fix to verbose (defaults to false now) option and title for mask The following has been information is copied directly from the header of Wilkinson's rats.c. --------------------------------------------------------------------- module rats.h: implements RATS algorithm for local, bilevel thresholding, using square-sobel filtering References: M.H.F. Wilkinson (1998) Optimizing edge detectors for robust automatic threshold selection. Graph. Models Image Proc. 60: M.H.F. Wilkinson (1996) Rapid automatic segmentation of fluorescent and phase-contrast images of bacteria. In: Fluorescence Microscopy and Fluorescent Probes, (J. Slavik, ed), pp 261-266, Plenum Press, New York. Author: Michael H. F. Wilkinson Institute for Mathematics and Computing Science University of Groningen, PO Box 800, 9700 AV Groningen, The Netherlands e-mail: michael@cs.rug.nl Version: 14-04-2000 Comments: Feel free to use non-commercially, but do acknowledge copyright, or (even better) cite articles above :-) --------------------------------------------------------------------- To the above references please add... M.H.F. Wilkinson "Segmentation Techniques in Image Analysis of Microbes" which is chapter 3 in Digital Image Analysis of Microbes: Imaging, Morphometry, Fluorometry and Motility Techniques and Applications. Edited by M.H.F. Wilkinson and F. Schut, Wiley Modern Microbiology Methods Series (1998).