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

Posted by Stoyan Pavlov on Aug 09, 2011; 8:42am
URL: http://imagej.273.s1.nabble.com/Measure-intensities-on-rather-than-within-an-ROI-line-and-be-able-to-specify-the-line-width-tp3683556p3683562.html

Hi Emmanuel,
I had a similar problem and used the following macro to generate
pericellular Rois from a set of oval rois (cell borders):


n = roiManager("count");
  for (i=0; i<n; i++)  {
roiManager("select", i);
run("Fit Spline");
run("Make Band...", "band=1");
run("Enlarge...", "enlarge=7");
roiManager("Update");
}
  The macro transforms the border into a band and then enlarges it in
and out by 3 px and then updates the Roi in the set.
You can manipulate these values by changing the 7 to any odd integer.

I hope this will help.

Stoyan

2011/8/9 Emmanuel Levy <[hidden email]>:

> 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
>

--
Dr. Stoyan P. Pavlov, MD
Departament of Anatomy, Histology and Embryology
Medical University "Prof. Dr. Paraskev Stoyanov", Varna
Prof. Marin Drinov Str.55
9002 Varna
 Bulgaria
Tel: +359 (0) 52 - 677 - 050 #2638
e-mail: [hidden email]