Posted by
vytas-2 on
Jul 24, 2006; 12:02pm
URL: http://imagej.273.s1.nabble.com/Analyze-Particles-Issue-tp3702049p3702050.html
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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