Re: Automatic ROI for particle anamysis

Posted by Arne Seitz on Jul 28, 2011; 1:39pm
URL: http://imagej.273.s1.nabble.com/Automatic-ROI-for-particle-anamysis-tp3683626p3683627.html

Hi Samuel,

Here is the way I would do it.

- Take your image of the nucleus and threshold it (if the SNR is low you can first apply a mean or gaussian filter).
- On the thresholded image run Analyze-->Analyze Particles...
- Check "Add to Manager"

This will add every nucleus as a single ROI to the roi manager. Now you can measure the intensities of the ROIs individual or all at once in the red and the green channel.

I hope that helps.

Cheers Arne

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> samuel collombet
> Sent: jeudi 28 juillet 2011 12:53
> To: [hidden email]
> Subject: Automatic ROI for particle anamysis
>
> Hi,
>
> I have RGB pictures from nucleus staining and I would like to measure
> the ratio of red and green staining in each nucleus. My way of doing it
> so far was to draw manually a ROI around each nucleus and measure the
> intensity with /analyse/measure/.
>
> My question is : is there a plugin/macro to automatically creat ROI
> around all nucleus (I have thought to threeshold my picture, apply a
> granulometric filter and import this new picture as an ROI, but I
> couldn't found any way to do that) but with independant ROI for each
> nucleus, to be able to have a measure for each?
>
>
> Thanks,
> Samuel
>
> --
> Samuel Collombet
> [hidden email]
> 237 B/6 Gilmerton Road, EH16 5TH Edinburgh