ROI with holes / Particle Analyzer vs. ROI Manager

[Niko Ehrenfeuchter]

Dear all,

the Particle Analyzer can "exclude" holes when measuring particles,
gives reasonable results on my data.

However, when using the "Add to Manager" option that creates a new ROI
for every particle in the ROI Manager, these holes seem to be ignored -
when measuring the ROI's (the ones that got added by the Particle
Analyzer) from the ROI Manager, the "area" value clearly indicates that
the holes were included in those ROIS. Unlike requested in the Particle
Analyzer.

Is there any way around this?

Thanks,
~Niko
--
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University
of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
Phone: [phone] | [hidden email] |
www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Rasband, Wayne (NIH/NIMH) [E]]

On Oct 3, 2014, at 5:52 AM, Niko Ehrenfeuchter wrote:

> Dear all,
>
> the Particle Analyzer can "exclude" holes when measuring particles, gives reasonable results on my data.
>
> However, when using the "Add to Manager" option that creates a new ROI for every particle in the ROI Manager, these holes seem to be ignored - when measuring the ROI's (the ones that got added by the Particle Analyzer) from the ROI Manager, the "area" value clearly indicates that the holes were included in those ROIS. Unlike requested in the Particle Analyzer.
>
> Is there any way around this?

Enable "Limit to threshold" in Analyze>Set Measurements and the Particle Analyzer and ROI Managers measurements will be the same. The following example macro enables the "Limit to threshold" option, creates a blank image, adds two particles with holes, thresholds the image, runs the Particle Analyzer and measures the two particles in the ROI Manager.

-wayne

  run("Set Measurements...", "area mean limit display decimal=3");
  newImage("Untitled", "8-bit black", 500, 500, 1);
  makeOval(73, 51, 168, 154);
  run("Invert");
  makeOval(121, 89, 83, 84);
  run("Invert");
  makeOval(254, 250, 165, 182);
  run("Invert");
  makeOval(300, 305, 74, 78);
  run("Invert");
  run("Select None");
  setAutoThreshold("Default dark");
  run("Analyze Particles...", "display clear add");
  roiManager("Measure");

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[Niko Ehrenfeuchter]

Thanks, Wayne!

On 05.10.2014 19:33, Rasband, Wayne (NIH/NIMH) [E] wrote:

> On Oct 3, 2014, at 5:52 AM, Niko Ehrenfeuchter wrote:
>
>> Dear all,
>>
>> the Particle Analyzer can "exclude" holes when measuring particles, gives reasonable results on my data.
>>
>> However, when using the "Add to Manager" option that creates a new ROI for every particle in the ROI Manager, these holes seem to be ignored - when measuring the ROI's (the ones that got added by the Particle Analyzer) from the ROI Manager, the "area" value clearly indicates that the holes were included in those ROIS. Unlike requested in the Particle Analyzer.
>>
>> Is there any way around this?
>
> Enable "Limit to threshold" in Analyze>Set Measurements and the Particle Analyzer and ROI Managers measurements will be the same. The following example macro enables the "Limit to threshold" option, creates a blank image, adds two particles with holes, thresholds the image, runs the Particle Analyzer and measures the two particles in the ROI Manager.
>
> -wayne
>
>    run("Set Measurements...", "area mean limit display decimal=3");
>    newImage("Untitled", "8-bit black", 500, 500, 1);
>    makeOval(73, 51, 168, 154);
>    run("Invert");
>    makeOval(121, 89, 83, 84);
>    run("Invert");
>    makeOval(254, 250, 165, 182);
>    run("Invert");
>    makeOval(300, 305, 74, 78);
>    run("Invert");
>    run("Select None");
>    setAutoThreshold("Default dark");
>    run("Analyze Particles...", "display clear add");
>    roiManager("Measure");
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University
of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
Phone: [phone] | [hidden email] |
www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html