Posted by
Thomas Boudier on
Dec 09, 2014; 3:43am
URL: http://imagej.273.s1.nabble.com/count-nuclei-in-a-volume-tp5010848p5010854.html
Dear Cesar,
Maybe you can have a look to the cell segmentation challenge where
similar data are available, you will get an idea of what is possible.
But basically if your signal is quite homogeneous across the tissue, you
can use thresholding, then erosion to separate touching objects. More
complex procedures may be available, like 3D band pass filtering if your
object have constant size, or iterative thresholding for dealing with
difference in intensities, contact me for details.
http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:droplet_counter:starthttp://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:3d_spots_segmentation:startBest,
Thomas
On 09/12/14 03:08, Cesar Mendes wrote:
> Greetings,
>
> I want to count the number of nuclei in a tissue which express a nuclear marker (H2B:YFP). Is there a good way to do this automatically?
> Attached you can see a stack of one of these images. This is a low populated example, i have other genotypes that will be much more crowded and harder to count manually.
> I acquire data from a Leica confocal that can be converted to imageJ stacks.
> Some cells have a decreased level of the marker and that might be an issue.
> Thanks in advance!
> Best,
> Cesar
>
>
>
>
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Thomas Boudier, Associate Professor, UPMC,
Université Pierre et Marie Curie, Paris, France.
BioInformatics Institute (BII)/IPAL, Singapore.
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