Analyze, Particles gives strange results

Hi,
I’m getting strange results when I use Analyze, Particles on the attached image. When I run the following code on it:

importClass(Packages.ij.IJ);
importClass(Packages.ij.plugin.frame.RoiManager);
importClass(Packages.ij.io.OpenDialog);
importClass(Packages.ij.io.DirectoryChooser);
importClass(Packages.java.io.File);
importClass(Packages.ij.gui.GenericDialog);
importClass(Packages.ij.util.Tools);
importClass(Packages.ij.plugin.Duplicator);
importClass(Packages.ij.measure.ResultsTable);
importClass(Packages.ij.ImagePlus);
importClass(Packages.ij.process.ImageProcessor);
importClass(Packages.ij.util.ArrayUtil);
importClass(Packages.ij.gui.Overlay);
importClass(Packages.ij.plugin.filter.ParticleAnalyzer);
importClass(Packages.ij.gui.Roi);
importClass(Packages.ij.plugin.filter.Analyzer);
importClass(Packages.ij.plugin.RGBStackMerge);
importClass(Packages.ij.process.ImageConverter);
importClass(Packages.ij.gui.OvalRoi);
importClass(Packages.ij.WindowManager);
importClass(Packages.ij.ImageStack);
importClass(Packages.ij.gui.ProfilePlot);
importClass(Packages.ij.gui.Line);
importClass(Packages.ij.gui.Plot);
importClass(Packages.ij.measure.CurveFitter);
importClass(Packages.ij.plugin.frame.Fitter);
importClass(Packages.ij.gui.PolygonRoi);
importClass(Packages.ij.process.ImageStatistics);
importClass(Packages.ij.measure.Measurements);
importClass(Packages.ij.plugin.ZProjector);
importClass(Packages.ij.gui.ShapeRoi);
importPackage(java.awt);

imp = IJ.getImage();
IJ.run(imp, "Set Scale...", "distance=0");
rm = RoiManager.getInstance();
if (rm==null) rm = new RoiManager();
IJ.run("ROI Manager...", "");
IJ.run("To ROI Manager", "");
rm.select(0);
IJ.setThreshold(imp, 105, 362);
IJ.run(imp, "Analyze Particles...", "size=50-Infinity display add");

I get one new Roi that resulted from Analyze, Particles. The strange thing about this Roi is that it is identical to the original Roi that was segmented. I would expect the resulting Roi to be smaller. Can anyone understand why I’m getting such a strange result? I’m using ImageJ 1.51a13, java 1.6.0_65 on a mac OSX 10.9.5.

Thanks,
Avital

Thresh105to362.zip (3.6 MB)

Hello there, @Avital_Steinberg
I just ran used analyse particles on the whole image and got the area of the each round spot (below). Is this what you are interested in measuring? It seems to work fine for me

Thanks - this is not what I wanted to do, but my issue was resolved already using ImageJ’s mailing list: https://imagej.nih.gov/ij/list.html