Re: Cannot see "masked" result image from: IJ.run(imp, "Analyze Particles...", "show=Masks exclude clear");

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Re: Cannot see "masked" result image from: IJ.run(imp, "Analyze Particles...", "show=Masks exclude clear");

Guy Stysis
Hey all,

I was working with the java code of imagej and when I run:

IJ.run(imp, "Analyze Particles...", "show=Masks exclude clear");

I am unable to obtain the image output "masks" because it seems to be deep within the particle analyzer code and is never returned.

Thank you for your help!
Guy

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Re: Cannot see "masked" result image from: IJ.run(imp, "Analyze Particles...", "show=Masks exclude clear");

Wayne Rasband-2
On May 11, 2019, at 4:05 AM, Guy Stysis <[hidden email]> wrote:
>
> Hey all,
>
> I was working with the java code of imagej and when I run:
>
> IJ.run(imp, "Analyze Particles...", "show=Masks exclude clear");
>
> I am unable to obtain the image output "masks" because it seems to be deep within the particle analyzer code and is never returned.

The Analyze Particles option you are looking for is called “Count Masks”. This is what was recorded when I opened the “Blobs” sample image, ran the particle analyzer, applied the “Viridis” lookup table and set the display range to 0-64:

  run("Blobs (25K)");
  setAutoThreshold("Default");
  run("Analyze Particles...", "  show=[Count Masks] display clear");
  run("Viridis");
  setMinAndMax(0, 64);

-wayne

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