Automated cell counter for immunostained cells

[csadangi]

Hi,

I want to count the number of cells in my immunostained tissues. I am looking for an automated counter which would do the counting once i select my region of interest (ROI). I have already come across the cell counter and ICTN plugin but that didn't help (ICTN) me a lot.

Any help would be highly appreciated.

Cheers

[G. Esteban Fernandez]

Sounds like you're not working with fluorescence.  For traditional color
stains I use the Colour Deconvolution plugin to separate the channels and
then threshold to count cells with Analyze Particles (after some processing
like Watershed segmentation). Usually this is for DAB-stained tissue
counterstained with hematoxylin, so I use the "H DAB" color matrix in
Colour Deconvolution or define my own.

To automate this I record the steps into a macro.

-Esteban
On Oct 4, 2014 9:04 AM, "csadangi" <[hidden email]> wrote:

> Hi,
>
> I want to count the number of cells in my immunostained tissues. I am
> looking for an automated counter which would do the counting once i select
> my region of interest (ROI). I have already come across the cell counter
> and
> ICTN plugin but that didn't help (ICTN) me a lot.
>
> Any help would be highly appreciated.
>
> Cheers
>
>
>
> -----
> ----
> Chinmaya
> Medical University Innsbruck
> Innsbruck
> Austria
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Automated-cell-counter-for-immunostained-cells-tp5009904.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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[sarahmmph]

Hi Esteban,
did you use the built-in vectors fro color deconvolution? or you made your own vectors?

Sarah

[G. Esteban Fernandez]

Mostly the built-in ones but sometimes my own.  The trouble I run into
is slide-to-slide variation in staining, so sometimes I have to use
more than one custom vector for different batches of stainings.

-Esteban

On Tue, Oct 7, 2014 at 8:42 AM, sarahmmph
<[hidden email]> wrote:

> Hi Esteban,
> did you use the built-in vectors fro color deconvolution? or you made your
> own vectors?
>
> Sarah
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Automated-cell-counter-for-immunostained-cells-tp5009904p5009942.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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[Jacqueline Ross]

Hi All,

If anyone is interested, I've recently updated my instructions for using the Colour Deconvolution plugin.

Take a look here: https://www.fmhs.auckland.ac.nz/en/sms/about/our-departments/biomedical-imaging-research-unit/image-processing-and-analysis/analysis-resources.html

The instructions for creating a macro when you need to create your own vectors using user values are from last year but should work fine. I also have a macro for batch processing, which saves the images you want, if anyone is interested. I haven't uploaded it to our site yet.

Of course, it's always better to create these vectors from slides with single stains first...

Kind regards,

Jacqui

Jacqueline Ross
Biomedical Imaging Microscopist
Biomedical Imaging Research Unit 
School of Medical Sciences 
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland 1142, NEW ZEALAND

Tel: [phone]
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of G. Esteban Fernandez
Sent: Wednesday, 8 October 2014 5:26 a.m.
To: [hidden email]
Subject: Re: Automated cell counter for immunostained cells

Mostly the built-in ones but sometimes my own.  The trouble I run into is slide-to-slide variation in staining, so sometimes I have to use more than one custom vector for different batches of stainings.

-Esteban

On Tue, Oct 7, 2014 at 8:42 AM, sarahmmph <[hidden email]> wrote:

> Hi Esteban,
> did you use the built-in vectors fro color deconvolution? or you made
> your own vectors?
>
> Sarah
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Automated-cell-counter-for-immunostai
> ned-cells-tp5009904p5009942.html Sent from the ImageJ mailing list
> archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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