Re: Attachmentpoints and Endpoint-problem

Posted by maringa on
URL: http://imagej.273.s1.nabble.com/Attachmentpoints-and-Endpoint-problem-tp3692095p3692097.html

Hi Michael,

I have tried these methods you suggested, but in 1) It only generates
random dots, and very few of them aswell. I tried with a neurite-stained
hippocampal image and a neurite stained P19 image but I only get 10-30
random dots. I skeletonize, set cound, erode and then subtract.

As for 2) I also get few and random dots even though I skeletonize, count
6, erode.

I dont quite know what could be the problem here...

Maringa

>
> Hi Maringa,
>
> 1) skeltonize first, then duplicate, set "count" in Binary Options to
> 7 and erode. Subtract the two - this should give you the endpoints.
>
> 2) skeletonize, set "count" in Binary Options to 6 and erode. This
> leaves only the crossings. Note that crossings under an oblique angle
> will usually result in two points; you can combine them 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).
>
> Michael
> ________________________________________________________________
>
> On 15 Jun 2009, at 04:31, maringa wrote:
>
>> Hi there,
>>
>> I'm working with neurons and right now I'm stuck on one and a half
>> problem.
>> 1) Endpoint-detection of the neurites, working so so... (image)
>> http://img191.imageshack.us/img191/433/endpoints.jpg
>>
>> My idea was to first remove the cellbodies, leaving the image with
>> just
>> neurites, and
>> then erode by 1px (the neurites gets 1px shorter) and then
>> skeletonize. This
>> image
>> is then subtracted from a copy of this skeletonized image, but the
>> copy is
>> not eroded
>> so the subtraction results in small dots which I hoped to be the
>> endpoints.
>> Turned out to be a lot more irrellevant dots than I wanted...
>>
>> 2) Attachmentpoints.
>>
>> My idea here was to use dilate-filter, dilate the neurites by a
>> couple of
>> pixels to generate a cross
>> where it enters the cellbody. Then use some kind of transformation
>> to count
>> the crosses... is this possible in the first place?
>>
>> There are a lot of problems associated with this, for example it's
>> really
>> hard to make a nice cross...
>>
>> Any ideas on this? It really got me stuck for a couple of weeks...
>
>
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