Problem with getting XStart

[AndersS]

Hello!

I have a problem when I try to analyze my images in ImageJ.
I run the line

run("Analyze Particles...", "  show=Outlines display clear record");

and save my results

saveAs("Results", imageName+".txt");

But when I extract the give XStart from the results it gives me what X is where YStart starts.
example image:


Is there a solution to this problem, or have I just done something wrong?

[Jan Eglinger]

Hi AndersS,

On 17.07.2014, 5:00 PM, AndersS wrote:

> I have a problem when I try to analyze my images in ImageJ.
> I run the line
>
> run("Analyze Particles...", "  show=Outlines display clear record");
>
> and save my results
>
> saveAs("Results", imageName+".txt");
>
> But when I extract the give XStart from the results it gives me what X is
> where YStart starts.
> example image:
> <http://imagej.1557.x6.nabble.com/file/n5008803/wat.jpg>
>
> Is there a solution to this problem, or have I just done something wrong?
>

... [show rest of quote]

XStart and YStart serve the purpose of re-creating a particle from a
mask after "Analyze Particles", since the point (XStart, YStart) is
guaranteed to be *inside* the particle.

What you want is most likely the dimensions of the bounding rectangle
that you get by activating 'Bounding rectangle' in the 'Analyze > Set
Measurements...' dialog. It will record BX and BY, the coordinates of
the upper left corner of the rectangle, with BX being the value you want.

See the documentation:
http://imagej.nih.gov/ij/docs/guide/146-30.html#sub:Set-Measurements...

Cheers,
Jan

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

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

On Jul 17, 2014, at 11:00 AM, AndersS wrote:

> Hello!
>
> I have a problem when I try to analyze my images in ImageJ.
> I run the line
>
> run("Analyze Particles...", "  show=Outlines display clear record");
>
> and save my results
>
> saveAs("Results", imageName+".txt");
>
> But when I extract the give XStart from the results it gives me what X is
> where YStart starts.
> example image:
> <http://imagej.1557.x6.nabble.com/file/n5008803/wat.jpg>

... [show rest of quote]

(XStart,YStart) are the coordinates of the first boundary point of particles found by the particle analyzer, not the coordinates of the left-most point. The following example macro finds the left-most points. If a particle has multiple left-most points, the top one is used.

The particle analyzer's "Record starts" option is obsolete. It has been replaced by the "Overlay Outlines" (used by this macro) and "Add to Manager options.

  run("Blobs (25K)");
  setAutoThreshold("Default");
  run("Analyze Particles...", "size=100 show=[Overlay Outlines] exclude");
  n = Overlay.size;
  run("Clear Results");
  for (i=0; i<n; i++) {
      Overlay.activateSelection(i);
      getSelectionCoordinates(xpoints, ypoints);
      x=9999; y=9999;
      for (j=0; j<xpoints.length; j++) {
         if (xpoints[j]<=x) {
            x = xpoints[j];
            y = ypoints[j];
         }
      }
      setResult("X", i, x);
      setResult("Y", i, y);
   }
   updateResults;


> Is there a solution to this problem, or have I just done something wrong?
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Problem-with-getting-XStart-tp5008803.html
> Sent from the ImageJ mailing list archive at Nabble.com.

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

[AndersS]

Thank you both for your answers! They were very helpful.