Re: Help: Centrosome quantification

Posted by karo03 on Jul 29, 2010; 9:32am
URL: http://imagej.273.s1.nabble.com/Help-Centrosome-quantification-tp3687435p3687439.html

Hi Ignacio,
a straight forward solution, at least with your example might be:
- Segment nuclei in DAPI, cut 'connected' nuclei with watershed.
  This will deliver errors, either acceptable or to be corrected!
- Skeletonize the inverted resulting nuclei image, possibly reduced by black background (see attachment)
  Some cleaning delivers 'cell' areas allowing to count particles per cell area:
  - First measure these 'cell' areas with add to ROI Manager
  - Segment the particles
  - Update/Adjust ROIs to the intersecting particles, this will lead to ROIs per cell area of the particles
macro "ROIAdjustLabel_" {
// Given: A binary Image with components (selected)
//           roi's (ROImanager) (typically larger than the image components)
// Result: rois are updated to the intersection of the roi and the binary image
//             Label numbers of the rois are transfered to the intersecting parts
//             for further analysis
//
 setBatchMode(true);
 title = getTitle();
 run("Select None");
 run("Duplicate...", "title=tmp");
 run("Select All");
 run("Clear");
 run("Select None");
 ct=roiManager("count");
 for (i=0;i<ct;i++){
    roiManager("Select", i);
    roiManager("Fill");
    imageCalculator("AND", "tmp", title);
    run("Make Binary");
    run("Create Selection");
    roiManager("Update");
    run("Clear");
    run("Select None");
 }
 close();
 setBatchMode(false);
}

Maybe this skeleton of method might help
Regards
Karsten

Am 28.07.2010 um 22:47 schrieb Ignacio Fernandez-Garcia:

> Hi all,
> Lately I've been working analyzing the centrosome abnormalities in some experiments. One thing we're interested in is the number of centrosomes per cell (usually two in normal cells). To detect the centrosomes we use an immunoflurescence technique where we label the centrosomes in green and counterstain the nuclei with DAPI in blue. So, we obtain images like this one:
>
> http://a.imageshack.us/img715/4948/tubulincaexample.jpg
>
> As you can see, we have some green signals (the punctual ones) distributed within the cell cytoplasm (seen as green background) but not necessarily within the nucleus. This way, a nuclear mask with the DAPI is not enough to segment the centrosomes and quantify them as a "number-of-centrosomes-per-cell" value.
> One approach that comes to my mind is: Segment both, centrosomes and nucleus, in their correspondent channel, and then associate the segmented centrosome signals with the nearest segmented nucleus by the minimum square distance between mass centers.
> So, my question is, anybody can help me with that? does anybody have done it before?
> Also I'll really appreciate suggestions, comments, questions, etc.
> Thanks!
> Cheers!

Karsten
[hidden email]