Hi Erong,
> I am trying to use ImageJ/Fiji to count cells stained for their nuclei
> that are only surrounded by a different stain. As such, I do not
> believe making the image binary will be the best option for me, as it
> will count all the cells, even the ones without the stain surrounding
> it.
The basic workflow is to first preprocess your image as needed, such that
applying a binary threshold will divide your objects and background
appropriately. Once you have a segmentation derived from the binary image,
you can apply it back to your original data to obtain your measurements.
For details, see:
http://imagej.net/SegmentationRegards,
Curtis
On Mon, Jan 12, 2015 at 2:28 PM, KerL <
[hidden email]> wrote:
> Dear all,
>
> I am trying to use ImageJ/Fiji to count cells stained for their nuclei that
> are only surrounded by a different stain. As such, I do not believe making
> the image binary will be the best option for me, as it will count all the
> cells, even the ones without the stain surrounding it.
> I have tried the plugin "Nucleus Counter" as an option but I have found
> that
> it uses 16-/8-bit images and therefore I cannot adjust for the color
> threshold. Also the shape of the cells I am counting are irregular and this
> plugin often mistakes 1 cell as 2 cells etc..
>
> Is there a different way of going about this task?
>
> Thank you in advance,
>
> Erong
>
>
>
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> View this message in context:
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http://imagej.1557.x6.nabble.com/Counting-nuclei-without-making-image-binary-tp5011196.html> Sent from the ImageJ mailing list archive at Nabble.com.
>
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