Re: soma area detection

Posted by Michael Schmid on Apr 20, 2011; 10:07am
URL: http://imagej.273.s1.nabble.com/soma-area-detection-tp3684897p3684901.html

Hi Quing,

As I am not a biologist I don't know what structures you want to  
extract from your image - I hope for the biologists on the list to  
solve that problem.

Concerning ImageJ vs. Matlab:
As far as I can say from the sample image on the MatLab site, the  
operation is exactly the same as minimum+maximum in ImageJ, but there  
is a slight difference of kernel size: Matlab says the radius is 5; I  
have to use a radius of 4.5 in ImageJ for the same result. This is  
not astonishing - there are different conventions for the radius.  
Otherwise, only the brightness&contrast of the output image has been  
readjusted to fit the 0-255 range of 8-bit data, then you get the  
same as on the Matlab site.

Michael
________________________________________________________________

On 19 Apr 2011, at 23:53, Qing Liu wrote:

> 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
>>>
>>