Re: Marking Cell Centroids in a Stack

Posted by Anthony Kowal on May 12, 2009; 7:40pm
URL: http://imagej.273.s1.nabble.com/Marking-Cell-Centroids-in-a-Stack-tp3692560p3692562.html

Hi Michael,

Thanks for the suggestions.  I am trying to analyze cells which are
chemotaxing towards folate, and my goal is to determine the velocity of the
cells, as well as compute a chemotactic index.  I have taken 30 to 40 minute
time lapse micrographs of these cells every 10 seconds.  For the analysis, I
am making a substack such that measurements are made every 30 seconds.  I am
using a program called MTrackJ (an Image J pluggin), but before I run
MTrackJ, I wish to mark the cell centroids (with a cross or dot), so that
when I am marking the cells I know that I am labeling the center of the
cell.

Thanks,
Tony



On 5/12/09, Michael Schmid <[hidden email]> wrote:

>
> 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.txt
> In 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
>>
>

--
Tony Kowal
Graduate Student
Chisholm Laboratory

Northwestern University
303 E. Superior
Lurie Building
Room 7-250
Chicago, IL 60611

Lab: 312 503 4169
e-mail: [hidden email]