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Measuring signal intensity from an area enclosed between two ROIs

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Avinash Kali

Measuring signal intensity from an area enclosed between two ROIs

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?

I know that by calculating the signal intensities from the two ROIs and using some simple math we can calculate the signal intensity from the area of interest. But this method may not be entirely correct.

Thank You.

Avinash.

dscho

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

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

Michael Schmid

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

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

Pål Baggethun

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

Also, if your ROI's are truly circular you can obtain normalized
integrated intenisties along concentric circles as a function of radius by
using the

Radial Profile Extended:
http://rsbweb.nih.gov/ij/plugins/radial-profile-ext.html

Pål Baggethun
Elkem Solar Research

Michael Schmid <[hidden email]>
Sent by: ImageJ Interest Group <[hidden email]>
29.10.2010 10:37
Please respond to
ImageJ Interest Group <[hidden email]>

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[hidden email]
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Subject
Re: Measuring signal intensity from an area enclosed between two ROIs

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:

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

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Cammer, Michael

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

In reply to this post by Avinash Kali

Before ImageJ had a band command, we would measure the big shape (intensity1 X area1) and then measure the small shape (intensity2 X area2) and then subtract the small shape's integrated intensity from the from the big shape's and divide by the difference of the areas area to get the band mean.

_________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: (212) 263-3208 Cell: (914) 309-3270

________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Avinash Kali [[hidden email]]
Sent: Friday, October 29, 2010 2:06 AM
To: [hidden email]
Subject: Measuring signal intensity from an area enclosed between two ROIs

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?

I know that by calculating the signal intensities from the two ROIs and using some simple math we can calculate the signal intensity from the area of interest. But this method may not be entirely correct.

Thank You.

Avinash.

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