Re: ParticleAnalyzer class and stacks

Posted by Rasband, Wayne (NIH/NIMH) [E] on Jul 06, 2014; 8:57pm
URL: http://imagej.273.s1.nabble.com/ParticleAnalyzer-class-and-stacks-tp5008596p5008597.html

On Jul 6, 2014, at 6:24 AM, Aryeh Weiss wrote:

> I am trying to use the particle analyzer in python. I found an example for use of the PA on stacks, in which the PA is run on each slice individually within a loop. Is there a way to run the PA on the entire stack, without having to loop over each slice?
> I looked for an example of this, and I am sure there must be many such examples, but I did not find it.

Try using the command recorder (Plugins>Macros>Record). The following is what is recorded when I open the "Bat Cochlea Volume" sample stack, threshold it and run the particle analyzer, with the recorder running in "JavaScript" mode.

  IJ.run("Set Measurements...", "area centroid stack decimal=3");
  imp = IJ.openImage("http://imagej.nih.gov/ij/images/bat-cochlea-volume.zip");
  IJ.setAutoThreshold(imp, "Default dark");
  IJ.run(imp, "Analyze Particles...", "size=10 display clear summarize stack");

-wayne
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