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

Posted by ERIC on May 26, 2014; 7:51pm
URL: http://imagej.273.s1.nabble.com/Problem-with-automated-cell-counting-for-DAB-stained-Fos-cells-in-brain-slides-tp5007921p5007936.html

Eric Denarier
Grenoble Institut des Neurosciences
Inserm U836
Chemin Fortuné Ferrini
38700 La Tronche
France


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Le 26/05/2014 16:58, Praz Nina a écrit :
> 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?
Yes we have been using this on IHC on brain slices to compare different
treatment.
You may have to work around the parameters because the FFT filter should
be adapted to the size of your nuclei.
You may also be interested by Daniel Sage's plugin  LoG3D :
http://bigwww.epfl.ch/sage/soft/LoG3D/
Of course I am afraid you will never get "The real number of nuclei"
because any image analysis will make errors that you can compensate by
the number of treated images...

> 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).
>>>
>>>
>>>
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