ParticleAnalyzer output in Java does not agree with program

Posted by Cspr on Mar 01, 2010; 7:10pm
URL: http://imagej.273.s1.nabble.com/ParticleAnalyzer-output-in-Java-does-not-agree-with-program-tp3689167.html

Hey everyone.

My problem is this. Using the macro:

IJ.run("Analyze Particles...", "size=0.15-Infinity circularity=0-1 show=Nothing display exclude clear include record add");

I'm greeted with the ROI manager and the results of applying these inputs. This is called from within Java, and the problem is that the results displayed (area, min_max, std_dev and so forth) is NOT the same that ImageJ gives back when using ImageJ. That is to say, when using ImageJ like you would any other program following the exact same steps results in something different than what results from using above command (with appropriate pre-steps before to the two procedures are identical up until that point).

For instance filling in the size field in the Analyze Particle dialog as 0.15-infinity is VERY different from the above command with size set as "size=0.15-999999". Using the first ("0.15-infinity") gives me back 87 measurements, whereas the exact same command called from within Java gives me 411 measurements.

I'm workin on images where the scale is 36 by 36 microns or 512 x 512 image. I think its a scale or calibration issue because everything up until that point is exactly what it should be.

Can anyone shed some light on what the problem is?

Thanks :)