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Re: cell by cell local thickness

Posted by Eric BADEL-2 on Mar 16, 2009; 3:15pm
URL: http://imagej.273.s1.nabble.com/cell-by-cell-local-thickness-tp3693294p3693298.html

- When I apply these plugin to the boundaries images, it works as if the ROI is the total cell (and not only the boundary).
- I'd like to get the whole list of the grey level values of each cell boundary.

One idea could be a macro that uses BinaryLabel8. Something like this (that does not still fully work ...)
On the binary boundary image:

run("BinaryLabel8 ", "white"); // generate "Labelled"
//run("Clear Results");
for (i=1; i<nResults+1; i++) {
   selectWindow("Labelled");
   run("Duplicate...", "title=Labelled-1");
   setThreshold(i, i);
   run("Convert to Mask");
   run("Create Selection");  
   getSelectionCoordinates(x, y);
   n = x.length;
   imageCalculator("AND create 32-bit", "LocalThickness.tif","Labelled-1"); // grey values of one boundary  (here "LocalThickness" is the LT image)
   for (j=0; j<n; i++) {
              v = getPixel(x[j], y[j]);
              setResult(i, x[j], y[j] , v ); // this line brings an error message ("," missing !!)
    }
   selectWindow("Labelled-1");
   run("Close" );
}
updateResults();

Any idea to correct this ?
Thank you.
Eric

Gabriel Landini a écrit :

> On Monday 16 March 2009 08:50:00 Eric Badel wrote:
>  
>> I generated an image that represents only the boundaries of the cell.
>> The grey level values on this boundary represent the corresponding local
>> thickness. Nox, I need to get these values, cell by cell. That means
>> that the boundary line should be one ROI. Nevertheless, if I try to get
>> values of this ROI, ImageJ thinks that the ROI is the surface of the shape.
>> How, could I define only the boundary as an ROI (and get all the
>> corresponding grey level value) ?
>>    
>
>
> What results do you want from those boundaries?
>
> You could use the particles8 plugin on the binary boundaries images and
> redirect to the distance transform image.
> The mean, mode, max, min, sd, etc of those distance transform pixels
> corresponding to the binary image will be collected in the Results window, one
> row per cell.
>
> I hope this helps.
> G.
>  

--
Eric BADEL

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BADEL Eric
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