Particle analysis in ROI

[ludwiczakagnieszka]

Cheers.
I'm trying to analyze the intramuscular fat particles on a cross-section of  a musce. I have already tried to apply "Analyze particles" but it refers to the whole image, not just the region of the muscle that I'm interested in. I want to analyze only the region within the boundary of the examined muscle - in order to get data on the distribution and shape of the fat particles as well as the percentage share of fat on the muscle cross-section surface. I suppose that I should use the ROI manager, but it doesn't offer an accurate particle anaysis. At least I can't find a way to link the ROI manager and the particle analysis.
I've attached an image (meat selected.png) after the muscle selection and using the "Clear outside" - as I've mentioned before, I'm interested in the muscle tissues only. I've also attached an image after convertion to 16-bit, thresholding, and "analyze particles" (particles.png). These particles are the subject of my research.
I will be gratefull for all guidelines.

[Aryeh Weiss]

On 6/18/14, 3:15 PM, ludwiczakagnieszka wrote:

> Cheers.
> I'm trying to analyze the intramuscular fat particles on a cross-section of
> a musce. I have already tried to apply "Analyze particles" but it refers to
> the whole image, not just the region of the muscle that I'm interested in. I
> want to analyze only the region within the boundary of the examined muscle -
> in order to get data on the distribution and shape of the fat particles as
> well as the percentage share of fat on the muscle cross-section surface. I
> suppose that I should use the ROI manager, but it doesn't offer an accurate
> particle anaysis. At least I can't find a way to link the ROI manager and
> the particle analysis.
> I've attached an image (meat selected.png) after the muscle selection and
> using the "Clear outside" - as I've mentioned before, I'm interested in the
> muscle tissues only. I've also attached an image after convertion to 16-bit,
> thresholding, and "analyze particles" (particles.png). These particles are
> the subject of my research.
> I will be gratefull for all guidelines.
>
>
> <http://imagej.1557.x6.nabble.com/file/n5008277/meat_selected.png>
> <http://imagej.1557.x6.nabble.com/file/n5008277/Particles.png>
>
>
>

If you have a ROI selected, the particle analyzer will only operate in
that ROI.

Here is an outline of how you might operate on a bunch of ROIs individually:


roiCount = roiManager("count");
for (i=0; i<roiCount; i++) {
     roiManager("select", i); // you need to select the ROI
     run("Analyze Particles...", "varius options go here"););

     and other stuff you need to do....
}

Of course, if you dont need to loop over your ROIs, you can do it once.

--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ludwiczakagnieszka]

Thank you very much for help.

Cheers,
Agnieszka.