Posted by
Michael Schmid on
URL: http://imagej.273.s1.nabble.com/Attachmentpoints-and-Endpoint-problem-tp3692095p3692096.html
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...