Re: generate ROIs around X,Y co-ordinate list

Posted by Schebique on Mar 27, 2009; 8:12am
URL: http://imagej.273.s1.nabble.com/Re-generate-ROIs-around-X-Y-co-ordinate-list-tp3693172p3693175.html

Hi.

may be you can find this code also usefull:

// This macro demonstrates how to add particle analyzer
// outlines to the ROI Manager. Note that doWand() may
// not work reliably unless the objects being traced
// have been highlighted in red using setThreshold().

requires("1.33f");
for (i=0; i<nResults; i++) {
    x = getResult('XStart', i);
    y = getResult('YStart', i);
    doWand(x,y);
    roiManager("add");
}


Damon Poburko napsal(a):

> Wayne Rasband wrote:
>>> Hi All,
>>>
>>>  I am trying to automate segmentation of small fluorescence events.
>>> In the process, I was planing on using the Analyze particles to help
>>> with this job. So far so good. But I am wondering how I might go
>>> about using the centroid X.Y position from the particle analysis to
>>> then go back and create ROIs of a predetermined size around the list
>>> of centroid co-ordinates. In theory this shouldn't be hard, but I'm
>>> at a loss for how to code it (i.e. gather the XY list from the
>>> results table and hand it to the ROI manager or generate regions).
>>
>> You can do this using a macro that retrieves the X and Y coordinates
>> from the Results table and uses them to generate ROIs of a
>> predetermined size. This example runs the particle analyzer on the
>> blobs sample image and, for each particle found, generates a radius
>> 15 circular ROI and adds it to the ROI Manager.
>>
>>   radius = 15;
>>   run("Blobs (25K)");
>>   setAutoThreshold();
>>   run("Set Measurements...", "area mean centroid redirect=None");
>>   run("Analyze Particles...", "size=0 circularity=0.00 display
>> exclude clear");
>>   resetThreshold();
>>   roiManager("reset");
>>   for (i=0; i<nResults; i++) {
>>      x = getResult("X", i);
>>      y = getResult("Y", i);
>>      makeOval(x-radius, y-radius, radius*2, radius*2);
>>      run("Add to Manager ");
>>   }
>>   setOption("Show All",true);
>>
>> -wayne
> Wayne & Chris,
>
> Perfect. That was exactly what I was looking for. That saved me a lot
> of time.
>
> Many thanks,
> Damon
>