Re: Problem with automated cell counting for DAB stained Fos+ cells in brain slides

Posted by Jacqueline Ross on May 27, 2014; 12:19am
URL: http://imagej.273.s1.nabble.com/Problem-with-automated-cell-counting-for-DAB-stained-Fos-cells-in-brain-slides-tp5007921p5007939.html

Hi Praz,

You could also try Subtract Background (e.g. radius 50) followed by the Find Maxima (e.g. Noise tolerance 45) as per Eric's suggestion. This worked well on your original image. Find Maxima is a really good option if you don't need to know the size/shape, etc. of the particles.

If you decide to use a threshold-based method, then I would use your negative control slide to set the threshold based on the background gray value (or measure an area on your image which is "unlabelled). Otherwise, it is very hard to decide what is really labelled and what isn't especially when doing manual counting.

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 Praz Nina
Sent: Tuesday, 27 May 2014 2:58 a.m.
To: [hidden email]
Subject: Re: Problem with automated cell counting for DAB stained Fos+ cells in brain slides

My mistake, I didn't invert the image... and also sharpened it, which probably made artifacts which were detected by finding maxima.

Thanks a lot Eric!

I'll try to optimize this, so it can be used throughout all sections, if it's possible! Does your lab use automated counting in this way?

And thanks again!

ERIC wrote

> Using the same method I found 215 nuclei.
> I don't understand where can come your result from. Sorry !!!
>
> I inverted the image after changing it to 8bits.
> There is maybe a difference in the binary options ( my settings are
> :Black is background)
>
> Eric Denarier
> Grenoble Institut des Neurosciences
> Inserm U836
> Chemin Fortuné Ferrini
> 38700 La Tronche
> France
>
>
> Tél :[phone]
> Fax :[phone]
>
> http://neurosciences.ujf-grenoble.fr/
>
> Le 26/05/2014 16:11, Praz Nina a écrit :
>> Also, I have tried to use your method on another image
>> (https://i.imgur.com/K9B3FnX.jpg)
>>
>> But I get something like 5000+ maxima, which doesn't correspond to
>> reality... (my manual counting says 247)
>>
>> For the automated counting, I don't know if it's possible, but the
>> point would be to use the same settings throughout the section/slide,
>> in order to remove as much variability as possible. Because if I have
>> to change the FFT bandpass for each image independently, that's
>> introducing a new variable..
>>
>> I've heard things about average threshold measure
>> (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803710/), but I haven't
>> been able to find the software to test it out (maybe it isn't the
>> best method).
>>
>>
>>
>> --
>> View this message in context:
>> http://imagej.1557.x6.nabble.com/Problem-with-automated-cell-counting
>> -for-DAB-stained-Fos-cells-in-brain-slides-tp5007921p5007927.html
>> Sent from the ImageJ mailing list archive at Nabble.com.
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
View this message in context: http://imagej.1557.x6.nabble.com/Problem-with-automated-cell-counting-for-DAB-stained-Fos-cells-in-brain-slides-tp5007921p5007932.html
Sent from the ImageJ mailing list archive at Nabble.com.

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

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