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Analyze Particles with results in pixel coordinates

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Analyze Particles with results in pixel coordinates

Stein Rørvik
Hello,

Is there any easy way to make Analyze Particles produce results in pixel coordinates on spatially calibrated images, besides making a duplicate image and removing the calibration on that? Or saving the current calibration, removing it, and then restoring it afterwards. Or making a macro that post-process the results.

Today, there is an option "Pixel units" in Analyze Particles. But that only affects the input size range. What I am looking for is a new checkbox like "Pixel unit results".

Stein

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Re: Analyze Particles with results in pixel coordinates

Rasband, Wayne (NIH/NIMH) [E]
On Jan 27, 2017, at 4:01 PM, Stein Rørvik <[hidden email]> wrote:
>
> Hello,
>
> Is there any easy way to make Analyze Particles produce results in pixel coordinates on spatially calibrated images, besides making a duplicate image and removing the calibration on that? Or saving the current calibration, removing it, and then restoring it afterwards. Or making a macro that post-process the results.
>
> Today, there is an option "Pixel units" in Analyze Particles. But that only affects the input size range. What I am looking for is a new checkbox like "Pixel unit results”.

Create a custom command that makes a copy of the image’s calibration, removes it from the image, runs the particle analyzer, then restores the calibration. Here is some JavaScript code that creates such a command:

   img = IJ.getImage();
   cal = img.getCalibration();  
   img.setCalibration(null);
   IJ.run(img, "Analyze Particles...", "");
   img.setCalibration(cal);

Save it in the ImageJ/plugins/Analyze folder as “Analyze_Particles_(pixels).js" to create a Plugins>Analyze>Analyze Particles (pixels) command.

-wayne

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