Posted by
Tiago Ferreira-2 on
Apr 02, 2014; 6:07pm
URL: http://imagej.273.s1.nabble.com/color-pixel-for-Strahler-order-tp5007132p5007185.html
On Apr 2, 2014, at 12:09, Gabriel Landini <
[hidden email]> wrote:
> Now seriously, I think that this problem could be resolved by a different
> means that does not require the skeleton encoded as a graph.
> Will post it if it works.
That would be great. Do let us know how it goes, and do let me know if I can
help.
Again, the .bsh script is not really sophisticated. It was born out of an
immediate need, so a different approach is more than welcome.
What the iterative pruning fails at is that it eliminates all terminal branches
indiscriminately, and thus it eliminates the root of the arbor upon the 1st pass.
This can be problematic. E.g. Take the example of a highly ramified neuronal arbor
shaped like a hand-held fan:
In such a structure, all processes branch out from a common focus (e.g., the cell
body). For biological meaningful Strahler orders, what would make sense would be
to always protect from elimination the endpoint at the cell body, so that orders
are really assessed in a centripetal manner, towards the soma.
At the time, I thought about prompting the user for an area ROI including the
'root' end-point to be protected, but it soon became clunky, and so, I've decided
to postpone it (so do let me know your suggestions and thoughts on this).
> Looking again
>
http://en.wikipedia.org/wiki/Strahler_number> I realised that they are shown as sub-branches. The confusing part is that the
> table counts all branches, not the order k ones, which appear as "end points".
>
> Perhaps it is the names of the columns that I could not relate to.
Oh, I see now how they can be misleading. I'll rename them to make it more clear,
and will try to output color-coded segments in a better way.
> Thanks for the follow up.
No thank you for looking into this.
-tiago
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