Posted by
Michael Schmid on
May 12, 2009; 4:43pm
URL: http://imagej.273.s1.nabble.com/Marking-Cell-Centroids-in-a-Stack-tp3692560p3692561.html
Hi Tony,
what do you think of, when you say "mark the centroids"? Draw a dot
there?
If you have a stack, you could write a simple macro that runs
"Analyze Particles" and has a loop over the particles with setPixel
(x,y) for each slice. See the nResults and getResult("Column", row)
macro commands.
If you have binary images, e.g. created by thresholding, the "Find
Maxima" function can create a point selection that marks the point
closest to the centroid of each particle (in contrast to the
centroid, this point never lies outside the particle bounds, even in
case of a slim crescent shape). You can transfer the point selection
to the original image by "Restore Selection" and use "Draw" to paint
the points in the foreground color.
For getting ideas how to do this in a stack, see, e.g., the
findStackMaxima macro
http://rsbweb.nih.gov/ij/macros/FindStackMaxima.txtIn your case, you will have to jump between the binary image and the
original, see the getImageID() and selectImage(id) macro functions.
I am not aware of a solution without a little bit of macro programming.
Hope this helps,
Michael
________________________________________________________________
On 12 May 2009, at 18:08, Anthony Kowal wrote:
> Hi Everyone,
>
> I am a novice at using ImageJ, and I have tried to find this answer
> out but
> with no success. I have taken a time lapse recording of cells
> chemotaxing
> towards folate, and am interested in not only finding the centroid
> of the
> cell, but also marking it in order to help with downstream
> analysis. Can
> anyone please point me in the right direction on how to do this?
>
> Thanks,
>
> Tony