Re: soma area detection

Posted by Qing Liu on Apr 19, 2011; 9:53pm
URL: http://imagej.273.s1.nabble.com/soma-area-detection-tp3684897p3684900.html

Hi, Michael,

Thank you for your suggestion. I am able to achieve better results with
Matlab morphological opening functions (strel and imopen):
http://www.mathworks.com/help/toolbox/images/ref/imopen.html.

With brightness/contrast/level adjustment in ImageJ and the morphological
opening settings in Matlab, I could suppress the neurites but the nuclei
seem to be problematic for applying threshold segmentation tool to measure
the soma size. Any suggestions for filling the holes/nuclei in the grayscale
image before the reconstruction? Thanks in advance.

Before: http://dl.dropbox.com/u/266880/start.tif
After: http://dl.dropbox.com/u/266880/MorphologicalOpening.tif

Qing


On Tue, Apr 19, 2011 at 4:39 AM, Michael Schmid <[hidden email]>wrote:

> 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
>>
>