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Attachmentpoint-problem

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maringa

Attachmentpoint-problem

Hi,

I posted a question a couple of weeks ago, about how to detect and count the attachmentpoints
of a soma (where the neurites attach to the soma) I got the advise to skeletonize two images, and
dilate or erode one of them with 1px and then subtract them from eachother. This just generates a lot of dots. I skeletonize, then set "count" in Binary Options to 6 and erode. Which should leave only the crossings. I also combined this by dilating with 'count=1' and 'iterations' a bit more than the line thickness.
Then run 'Find Maxima' to get single points or count the patches (former crossings).

However, the result is this:
http://img193.imageshack.us/img193/7715/neurph4.jpg
just a lot of small dots...

Does anyone have another sugestion? It's kind of annoying to be stuck whit this simple (?) problem...

Thanks in advance :)

Michael Schmid

Re: Attachmentpoint-problem

Hi Maringa,

can you post the binary input image to some server? (if it is too large,
don't scale it, crop it).
There are many ways to create the binary input from your color image.
Without seeing the binary image and trying for myself, I can't determine
the cause of the problem.

Michael
_____________________________________________________________________

On Wed, July 8, 2009 09:29, maringa wrote:

> Hi,
>
> I posted a question a couple of weeks ago, about how to detect and count
> the
> attachmentpoints
> of a soma (where the neurites attach to the soma) I got the advise to
> skeletonize two images, and
> dilate or erode one of them with 1px and then subtract them from
> eachother.
> This just generates a lot of dots. I skeletonize, then set "count" in
> Binary
> Options to 6 and erode. Which should leave only the crossings. I also
> combined this by dilating with 'count=1' and 'iterations' a bit more than
> the line thickness.
> Then run 'Find Maxima' to get single points or count the patches (former
> crossings).
>
> However, the result is this:
> http://img193.imageshack.us/img193/7715/neurph4.jpg
> just a lot of small dots...
>
> Does anyone have another sugestion? It's kind of annoying to be stuck whit
> this simple (?) problem...
>
> Thanks in advance :)
>

maringa

RE: Attachmentpoint-problem

Hi Michael,

Here is my binary image: http://img195.imageshack.us/img195/9354/20070510002005000i2max2.jpg

Maringa

Från: Michael Schmid-3 (via Nabble) [ml-user+[hidden email]]
Skickat: den 8 juli 2009 21:52
Till: Martina A K Johansson
Ämne: Re: Attachmentpoint-problem

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Michael Schmid

Re: Attachmentpoint-problem

Hi Maringa,

this image looks very different than your schematic drawing some two weeks
ago!
The main problem is identifying the soma. A very simple, but not very good
approach is simply binary "open" with a few iterations (e.g. 4) and the
default count=1. Update to the new ImageJ version 1.43c, then you can have
preview in the binary options and you see immediately what you get.
Run 'outline' on the soma.

Then skeletonize a copy of the input images, shorten the branches a bit
(erode with count=7, iterations e.g. 2) to get rid of noise.

Superimpose the skeletonized image and the soma outlines with the image
calculator 'average'. Threshold the 255 pixels - those should be roughly
where the dendrites attach to the soma. You can apply the selection and
use "find maxima" to get single points.

It is only a rough procedure, you will have to refine it. E.g. fewer
iterations for 'open' followed by the particle analyzer with a range of
circularity and size suited to better identify the soma. Also, replacing
"Open" with n iterations by Process>Filters>Minimum by a radius of n
pixels and then Maximum by the same number of pixels will better preserve
the shapes of the soma than 'open'.

Michael
_____________________________________________________________________

On Thu, July 9, 2009 06:41, maringa wrote:

> Hi Michael,
>
> Here is my binary image:
> http://img195.imageshack.us/img195/9354/20070510002005000i2max2.jpg
>
> Maringa
> ________________________________
>
>
> Hi Maringa,
>
> can you post the binary input image to some server? (if it is too large,
> don't scale it, crop it).
> There are many ways to create the binary input from your color image.
> Without seeing the binary image and trying for myself, I can't determine
> the cause of the problem.
>
> Michael
> _____________________________________________________________________
>
> On Wed, July 8, 2009 09:29, maringa wrote:
>
>> Hi,
>>
>> I posted a question a couple of weeks ago, about how to detect and count
>> the
>> attachmentpoints
>> of a soma (where the neurites attach to the soma) I got the advise to
>> skeletonize two images, and
>> dilate or erode one of them with 1px and then subtract them from
>> eachother.
>> This just generates a lot of dots. I skeletonize, then set "count" in
>> Binary
>> Options to 6 and erode. Which should leave only the crossings. I also
>> combined this by dilating with 'count=1' and 'iterations' a bit more
>> than
>> the line thickness.
>> Then run 'Find Maxima' to get single points or count the patches (former
>> crossings).
>>
>> However, the result is this:
>> http://img193.imageshack.us/img193/7715/neurph4.jpg
>> just a lot of small dots...
>>
>> Does anyone have another sugestion? It's kind of annoying to be stuck
>> whit
>> this simple (?) problem...
>>
>> Thanks in advance :)
>>