Re: vesicle distribution in cell population

Posted by Paul Grimm-2 on May 05, 2010; 5:22pm
URL: http://imagej.273.s1.nabble.com/vesicle-distribution-in-cell-population-tp3688365p3688369.html

Hi
That can be done with imageJ
Each cell that is identified as a mask can be identified and added to the ROI manager using the analyze particles function.

run("Analyze Particles...", "size=2000-75000 circularity=0.2-1.00 show=Nothing display exclude clear add");


You can then apply each particle (cell) one at a time as a SELECTION to your other image where the individual vesicles are identified.
something like this

selectImage("Cells");
print(title);

n = roiManager("count");
  for (z=0; z<n; z++) {
      roiManager("select", z);

   run("Copy");
selectImage("Vesicles");
   run("Restore Selection");
run("Analyze Particles...", "minimum=1 maximum=999999 bins=256 show=Nothing display clear");
cells=(nResults);
print(cells);
selectImage(""Cells");
}

This should give you an idea of the macro
--

Paul C. Grimm
Professor of Pediatrics
Dept of Pediatric Nephrology
Lucile Packard Children's Hospital
Stanford University School of Medicine
G306, MC 5208
300 Pasteur Drive
Stanford, CA 94305-5208
USA
phone   [phone]
fax       [phone]


In research, the present devours the past. Sir Peter Medawar

>
>
> Cosmin Mihai wrote:
>> Hi All,
>>
>> I have 2 D images of double stained cells - the cell membrane and some cytoplasmic vesicles – the number of which varies from cell to cell. Each image has 10-30 cells, and both the membrane stain and the vesicle stain can be easily segmented.
>> I am interested to extract a distribution of the vesicle number inside the individual cells at the cell population level, and to do that in an automatic fashion. I was thinking something along the lines of generating a mask from the membrane stain, registering the position and the outline of the cell area, and then apply that information to the image containing the vesicle stain in order to count and assign the number of vesicles to each cell.
>> Any ideas on to how to implement this with ImageJ?
>>
>> Thanks,
>> Cosmin
>>  
>
>
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