Re: Measuring signal intensity from an area enclosed between two ROIs

Posted by Michael Schmid on Oct 29, 2010; 8:37am
URL: http://imagej.273.s1.nabble.com/Measuring-signal-intensity-from-an-area-enclosed-between-two-ROIs-tp3686543p3686546.html

Hi Avinash,

there is also another possibility to select the area in ROI1 without  
that of ROI2:
Take ROI2 (inner circle), Make Inverse, add the result to the Roi  
Manager.
Then use AND of the ROI Manager with this Result and ROI1 (outer  
circle).

Michael
________________________________________________________________

On 29 Oct 2010, at 10:06, Johannes Schindelin wrote:

> Hi,
>
> On Fri, 29 Oct 2010, Avinash Kali wrote:
>
>> I am trying to measure the signal intensity from a ring-like  
>> structure
>> in my image.
>>
>> I drew an ROI enclosing the inner circle of the ring and another ROI
>> enclosing the outer circle of the ring. I have noticed that in ImageJ
>> 1.43 we can select multiple ROIs from ROI manager at the same  
>> time. This
>> makes the two ROIs appear at the same time on the image. But how  
>> can I
>> measure the signal intensity from the area enclosed between these two
>> ROIs?
>
> Actually, if you have a circular ROI enclosing another circular  
> ROI, you
> do not have a region _between_ them, but you have a region that is  
> only in
> one of them.
>
> The ROI Manager offers some operations to combine ROIs, such as AND
> (intersection) and OR (union), but not XOR (set difference). But  
> you can
> use this Javascript snippet to perform the operation:
>
> -- snip --
> importClass(Packages.ij.IJ);
> importClass(Packages.ij.gui.ShapeRoi);
> importClass(Packages.ij.plugin.frame.RoiManager);
>
> roiManager = RoiManager.getInstance();
> if (roiManager == null)
> IJ.showMessage("No ROI Manager present!");
> else {
> rois = roiManager.getSelectedRoisAsArray();
> if (rois.length != 2)
> IJ.showMessage("Need exactly two selected ROIs!");
> else {
> roi = new ShapeRoi(rois[0]);
> roi = roi.xor(new ShapeRoi(rois[1]));
> roiManager.addRoi(roi);
> }
> }
> -- snap --
>
> Just open an editor in ImageJ, paste the code, and run it via Run>Run
> Javascript (if I remember correctly; I use Fiji's script editor, of
> course).
>
> Before running it, you need to select exactly two ROIs in the ROI  
> Manager.
>
> Ciao,
> Johannes