Re: Measure intensities *on* rather than within an ROI line, and be able to specify the "line" width.

Posted by ctrueden on Aug 09, 2011; 2:19pm
URL: http://imagej.273.s1.nabble.com/Measure-intensities-on-rather-than-within-an-ROI-line-and-be-able-to-specify-the-line-width-tp3683556p3683560.html

Hi Emmanuel,

Directly on the ROI. The reason I'm using this is that both other
> solutions expand the ROI on the "outside" and I need to do it in the
> "inside". Thus I measure two areas and then make the difference
> between them to get the "band" information.
>

For interior bands, you can use the ROI Manager's XOR function. Here is a
small macro:

run("Add to Manager");
run("Enlarge...", "enlarge=-3");
run("Add to Manager");
roiManager("XOR");
roiManager("Deselect");
roiManager("Delete");

-Curtis

On Tue, Aug 9, 2011 at 1:27 AM, Emmanuel Levy <[hidden email]>wrote:

> Hi Lim and Curtis,
>
> Thanks a lot for your suggestions again.
>
> I've been playing around with this problem with a while and the first
> version that worked fine was to simply use:
>
> run("Enlarge...", "enlarge=-5");
>
> Directly on the ROI. The reason I'm using this is that both other
> solutions expand the ROI on the "outside" and I need to do it in the
> "inside". Thus I measure two areas and then make the difference
> between them to get the "band" information.
>
> The only problem is that calling this on all ROIs is really slow (I've
> got really a lot of them)!!
>
> I just saw the code of "shrink", which is part of the "enlarge" function:
>
> http://geosysin.iict.ch/irstv-trac/browser/imageJ/macros/EnlargeSelection.txt?rev=90
>
> And applying the trick from this function:
>
> run("Distance Map");
> setThreshold(5, 255);
>
> on my thresholded image seem to do the job very well. This means I'll
> just use two different images as "masks". One with the entire cells,
> and one where they are further thresholded based on the distance map.
>
> Emmanuel
>
>
>
> On 3 August 2011 23:24, Lim Soon Yew <[hidden email]>
> wrote:
> > Hi Emmanuel,
> >
> > You can try the macro I wrote below:
> >
> > p=2; //1-n Call ROI from ROI manager
> > l=5; //Line width for line profile
> > roiManager("Select", p-1); //index starts at 0)
> > //Extract points in ROI
> > getSelectionCoordinates(xCoordinates, yCoordinates);
> > makeSelection("polyline",xCoordinates, yCoordinates);
> > run("Line Width...", "line=l");
> > run("Plot Profile");
> >
> > Best Regards,
> > John
> > ________________________________________
> > From: ImageJ Interest Group [[hidden email]] On Behalf Of Emmanuel
> Levy [[hidden email]]
> > Sent: Wednesday, August 03, 2011 10:24 PM
> > To: [hidden email]
> > Subject: Measure intensities *on* rather than within an ROI line, and be
> able to specify the "line" width.
> >
> > Hi,
> >
> > I would like to measure pixel intensities along the border of
> > particles (cell membranes). In my macro each particle has a
> > corresponding ROI. That would be equivalent to being able to measure
> > the intensity *on* (and not within the ROI line), and be able to
> > specify the line width (e.g., 3-15 pixels).
> >
> > In principle this looks simple but I'm not sure what would be the best
> > way to achieve it. The simplest (and very rough) way I thought of was
> > to run every measure twice, one on the "dilated" particles and one on
> > the "eroded" same particles. However, it's not optimal if I want to
> > get measures for different widths simultaneously (e.g., 3,5,7,9,11,13
> > and 15 pixels "ribbon" width).
> >
> > Thanks for any advice you could give!
> > Best,
> >
> > Emmanuel
>