Counting Cells

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Counting Cells

Nadine Nahra
Good Morning,

I am working on a project with mice breast tissue, the slides have been stained using Immunohistochemistry IHC staining.
Is there any tool on ImageJ that I can use to count nuclei thats not by hand? Not sure who to contact about this but if anyone has answers it is greatly appreciated.
Thanks!

-Nadine
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Re: Counting Cells

Giorgio De Nunzio
Hi Nadine,
in this period I am working on object counting in microscopic images, in
different fields (not only cells) and with various tools (ImageJ,
matlab...). I am not an ImageJ expert so I cannot answer your question yet,
but I think that you could let people see some image example, so that we
can get an idea and someone can give an answer.
Thanks.
Giorgio

2018-05-16 17:05 GMT+02:00 Nadine Nahra <[hidden email]>:

> Good Morning,
>
> I am working on a project with mice breast tissue, the slides have been
> stained using Immunohistochemistry IHC staining.
> Is there any tool on ImageJ that I can use to count nuclei thats not by
> hand? Not sure who to contact about this but if anyone has answers it is
> greatly appreciated.
> Thanks!
>
> -Nadine
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Counting Cells

Citron, Bruce A.
Nadine and Giorgio-
The Multi-point tool under Tools provides a counter that can label objects and the Cell Counter plugin can do the same in different categories as you manually click/count.

for automated counting:
Only if the nuclei are making contact, you might need to Process- Binary- Make Binary and then Process- Binary- Watershed to separate them.

For counting of an 8-bit image, Image- Adjust- Threshold…- Adjust top slider until all nuclei are red and separated, then Analyze- Analyze Particles
   And you might select Display Results, Clear Results, Summarize, Adjust size range that will count,
   Adjust circularity to count (1.0= perfect circle, value =4 pi area/perimeter squared), May exlcued an cells touching the edge, Useful to Show Outlines of counted nuclei to compare to the original image
Then the summary can be saved in excel.

There are plugins that are useful for different types of fluorescent images, e.g., ShapeLogic  http://www.shapelogic.org/getting-started.html

Macros will be very useful to automate the process for a folder full of images.
-Bruce


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Re: Counting Cells

ctrueden
In reply to this post by Nadine Nahra
Hi Nadine,

Please take a look at https://imagej.net/Segmentation for an overview of
automated segmentation and counting techniques in ImageJ.

Regards,
Curtis


On Wed, May 16, 2018, 08:16 Nadine Nahra <[hidden email]> wrote:

> Good Morning,
>
> I am working on a project with mice breast tissue, the slides have been
> stained using Immunohistochemistry IHC staining.
> Is there any tool on ImageJ that I can use to count nuclei thats not by
> hand? Not sure who to contact about this but if anyone has answers it is
> greatly appreciated.
> Thanks!
>
> -Nadine
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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Re: Counting Cells

Robert Smith
Just a suggestion but if you go ahead and threshold the image you can use analyse  particles. that will usually count all the particles in the image.

I hope I understand what it is you are asking, but this always works for me.

Bob


________________________________
From: Curtis Rueden <[hidden email]>
Sent: Thursday, May 17, 2018 11:49 AM
To: [hidden email]
Subject: Re: Counting Cells

Hi Nadine,

Please take a look at https://imagej.net/Segmentation for an overview of
Segmentation - ImageJ<https://imagej.net/Segmentation>
imagej.net
Image segmentation is "the process of partitioning a digital image into multiple segments." (Wikipedia)



automated segmentation and counting techniques in ImageJ.

Regards,
Curtis


On Wed, May 16, 2018, 08:16 Nadine Nahra <[hidden email]> wrote:

> Good Morning,
>
> I am working on a project with mice breast tissue, the slides have been
> stained using Immunohistochemistry IHC staining.
> Is there any tool on ImageJ that I can use to count nuclei thats not by
> hand? Not sure who to contact about this but if anyone has answers it is
> greatly appreciated.
> Thanks!
>
> -Nadine
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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