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

Posted by dpoburko on Mar 26, 2009; 5:05pm
URL: http://imagej.273.s1.nabble.com/Re-generate-ROIs-around-X-Y-co-ordinate-list-tp3693172p3693174.html

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