Re: areatree results: LB cable length

Posted by Albert Cardona-2 on Jun 30, 2014; 9:14pm
URL: http://imagej.273.s1.nabble.com/areatree-results-LB-cable-length-tp5006194p5008505.html

2014-06-30 12:18 GMT-04:00 jrybak <[hidden email]>:

> I would like to measure the neuron length directly from the area list,
> that I
> reconstructed from serial EM sections.
> Is that possible ?
> I tried to export the area list as an Amira file. Here, I could convert the
> surface to a Skeleton.  but the file is label file too large, even with
> downsampling the export function uses (does she ?).
>
> Is there a way the area list, i.e the reconstructed neuron to convert to a
> construct, like a lineset, or Skeleton
> in order to read out parameters like neuron length, or make a dendrogramm
> ??
>
> Many thanks
> Jürgen
>
>
>

Jurgen,

to avoid creating an enormous image stack, one way to go about it is to
create an ImgLib image that uses a list of java.awt.Shape objects as the
data, rather than pixels. This is the approach taken for e.g. running
marching cubes on an AreaList [1]. With that ImgLib image, you could then
write a program to skeletonize it, which would be a generic ImgLib
algorithm--maybe it already exists, ask the ImgLib developers first.

An alternative that doesn't involve any code is to generate the labels
stack as a series of 2D images, and then open them as a virtual stack. The
performance of the skeletonizer will likely be poor, but it will do the job.

Best,

Albert

[1]
https://github.com/fiji/TrakEM2/blob/master/TrakEM2_/src/main/java/ini/trakem2/utils/AreaUtils.java#L124

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html