Analyze Particles Issue?

[Ankur Ramani]

Hello,

    I am having this problem with this macro I wrote. It works on stacks
of images and the purpose is to track cells as they migrate through a
gel through using the centroid. I am using the inbuilt Analyze particle
function to get my centroids; however, for some reason it is not picking
up all the thresholded objects, and seems to be only picking up ones
near the edges of the image. I am using a minimum area defined by the
user to limit the amount of cells shown. Also if anyone has any
suggestions for how to get ImageJ to define an object as the same object
in each slice (there are many cells in each picture which is a problem)
though I am still stuck on trying to get this part to work correctly.




Here is my code:

function Analyze_Stack()
{
    selectWindow("Reconstructed");
    run("Median...", "radius=1");  
    run("Set Scale...", "distance=1300 known=860 pixel=1 unit=microns
global");
    run("Set Measurements...", "area centroid display redirect=None
decimal=3");
O=1;
t=0;
for(n=1;n<=nSlices;n++)
{
        setSlice(n);
        O=1;
        while(O!=2)
        {
        min_area=newArray(20);
        if(t==0&&n==1)
            fin_area=getNumber("Minimum Area?: ", 100);
        else
          if(n==1)
            fin_area=getNumber("Minimum Area? (Previous was
"+min_area[t-1]+"):", 100);
       
        run("Analyze Particles...", "size="+fin_area+"-Infinity
circularity=0.00-1.00 show=Outlines display include record");
        t++;
        min_area[t]=fin_area;
        if(n==1)
        {
        O=getNumber("Redo Analysis? (1 for yes, 2 for no)", 1);
        }
        else
        O=2;

        if(O==1)
            {
            run("Close");
            selectWindow("Reconstructed");
            }
        else
            {
            saveAs("Jpeg");
            saveAs("Measurements");
            }
        }
    }
}

[vytas-2]

Try the 3D objects counter:
http://rsb.info.nih.gov/ij/plugins/track/objects.html
         It's a very useful and powerful tool for volumes (space or
time) with rich output. It counts each object only once (via centroids??).

At 09:00 AM 7/17/2006, you wrote:

>Hello,
>
>    I am having this problem with this macro I wrote. It works on
> stacks of images and the purpose is to track cells as they migrate
> through a gel through using the centroid. I am using the inbuilt
> Analyze particle function to get my centroids; however, for some
> reason it is not picking up all the thresholded objects, and seems
> to be only picking up ones near the edges of the image. I am using
> a minimum area defined by the user to limit the amount of cells
> shown. Also if anyone has any suggestions for how to get ImageJ to
> define an object as the same object in each slice (there are many
> cells in each picture which is a problem) though I am still stuck
> on trying to get this part to work correctly.
>
>
>
>
>Here is my code:
>
>function Analyze_Stack()
>{
>    selectWindow("Reconstructed");
>    run("Median...", "radius=1");
>    run("Set Scale...", "distance=1300 known=860 pixel=1
> unit=microns global");
>    run("Set Measurements...", "area centroid display redirect=None
> decimal=3");
>O=1;
>t=0;
>for(n=1;n<=nSlices;n++)
>{
>        setSlice(n);
>        O=1;
>        while(O!=2)
>        {
>        min_area=newArray(20);
>        if(t==0&&n==1)
>            fin_area=getNumber("Minimum Area?: ", 100);
>        else
>          if(n==1)
>            fin_area=getNumber("Minimum Area? (Previous was
> "+min_area[t-1]+"):", 100);
>
>        run("Analyze Particles...", "size="+fin_area+"-Infinity
> circularity=0.00-1.00 show=Outlines display include record");
>        t++;
>        min_area[t]=fin_area;
>        if(n==1)
>        {
>        O=getNumber("Redo Analysis? (1 for yes, 2 for no)", 1);
>        }
>        else
>        O=2;
>
>        if(O==1)
>            {
>            run("Close");
>            selectWindow("Reconstructed");
>            }
>        else
>            {
>            saveAs("Jpeg");
>            saveAs("Measurements");
>            }
>        }
>    }
>}
>
>

Vytas Bindokas, Ph.D.
Research Assoc. / Assoc. Prof.,
Director, BSD Light Microscopy Core Facility
Dept Neurobiol Pharmacol Physiol MC0926
947 E 58th Street
The University of Chicago
Chicago IL 60637
Room 1007 (CLSC)

773-702-4875

email [hidden email]
  web site for LMCF:
http://digital.bsd.uchicago.edu/index.html 



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