Re: Attachmentpoints and Endpoint-problem

Posted by Michael Schmid on Jun 18, 2009; 8:16am
URL: http://imagej.273.s1.nabble.com/Attachmentpoints-and-Endpoint-problem-tp3692095p3692098.html

Hi Maringa,

hard to say what is the problem without seeing the binary input  
image. Maybe 'skeletonize' creates a few short side branches that  
lead to the extra dots? You could get rid of them with count=7 and  
erode a few iterations; then skeletonize again. This will also reduce  
the length of the main branches, however.

There may be also a few helpful plugins on Gabriel Landini's page,  
e.g. some BinaryThin variations, see
   http://www.dentistry.bham.ac.uk/landinig/software/software.html

If you don't find a solution for the problem, post a binary input  
image to some server or send it to me off-list, and I could have a  
look at it (though not before tomorrow of Monday)

Michael
________________________________________________________________

On 18 Jun 2009, at 03:47, maringa wrote:

> 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...
>>
>>
>> ______________________________________
>>
>> This email is a reply to your post @
>> http://n2.nabble.com/Attachmentpoints-and-Endpoint-problem- 
>> tp3078257p3079946.html
>> You can reply by email or by visting the link above.
>>
>>
>
>
>
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