Posted by
Michael Schmid on
Apr 19, 2011; 8:39am
URL: http://imagej.273.s1.nabble.com/soma-area-detection-tp3684897p3684899.html
Hi Quing,
here is an attempt to translate the recipe into ImageJ commands:
Top-hat with circular kernel of radius r:
- duplicate the image
Assuming that your foreground objects have higher pixel value
than the background:
- Process>Filters>Minimum on the copy, radius r, followed by
- Process>Filters>Maximum on the copy, same radius r
- Image calculator to subtract the copy from the original
If your foreground pixel values are smaller than those of the
background, exchange Min&Max, and subtract the original from the copy.
Morphological opening:
- Process>Filters>Minimum with radius r1 (smaller than r for the top-
hat), then
- Process>Filters>Maximum with the same radius r1
Michael
________________________________________________________________
On 19 Apr 2011, at 00:39, Qing Liu wrote:
> Dear all, I have found a solution to select neuronal soma but need
> your
> suggestions to do so in imageJ.
>
>
http://dl.dropbox.com/u/266880/Soma.pdf>
> In the above paper, they mentioned
>
> the images of the neurons stained
>> for beta-III tubulin are first Gaussian filtered to suppress image
>> noise. They are background corrected using a top hat morphological
>> filter
>> with a disk structuring element larger than the
>> size of the largest cell body. A morphological opening
>> with a structuring element of a diameter smaller than the cell
>> body but larger than all neurites permits suppressing neuritelike
>> structures.
>>
>
> I am a little confused about the second and third step and wonder
> if anyone
> can help.
>
> Thank you.
>
> Qing