Dear Michel
One approach might be to convert your skeletonization to a distance map
[requires 0,255 values], threshold the map to the distance range you
want to count across, convert that to a mask, or selection, for
transfer/redirection to the 2nd channel. Make sure the distance map
reads as pixels to the outside of the structure. This is not so obvious
when setting up the distance map since inverted LUT commonly pops up on
binarized images.
Expect Z undercounts if you use a 2D distance map since your skeleton
will not extend into more than one focal plane. You will need a 3D
distance map to avoid this issue.
Why use the skeleton vs. the marker data directly? I would think the
latter will yield more precise measures.
cheers
On 8/10/2011 11:25 PM, Michel Herde wrote:
> Dear all,
> I want to analyze synaptic input onto a dendrite and have confocal image stacks with 2 channels, one with dendritic label and the other one labeling presynaptic boutons.
> My idea was to skeletonize the dendritic channel and then define a specific distance from the skeleton in which puncta in the synaptic channel can be counted.
> I managed to create a skeleton of the dendrite, however I'm stuck with further steps.
>
> Can I automatically create a selection at defined distance from the skeleton which I could then use on the synaptic channel?
> Or draw around the skeleton and then do an arithmetic subtraction from the synaptic channel?
>
> Any ideas welcome!
>
> Cheers
>
> Michel
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