Posted by
Kenneth Sloan-2 on
Aug 05, 2016; 12:42pm
URL: http://imagej.273.s1.nabble.com/From-3D-Projection-back-to-stack-tp5016974p5016980.html
You have a noise pixel in the projected image. That pixel will be either much lighter, or much darker, than it’s neighbors in the 2D projected image. In what follows, assume it’s lighter.
Now, consider the stack of voxels which contributed to that pixel. Which voxels are noise? Most likely the ones which are lighter than the other voxels in that stack.
Similarly, if you look at individual slices through the volume (parallel to the 2D projected image) you might look for voxels (from the column you are considering) that are lighter than their immediate neighbors (in the 2D slice).
It’s not perfect, but you miht find that it improves the skeleton. I’m not sure I would trust the edited volume all that much - but I suspect you will get a better skeleton.
--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.
> On Aug 4, 2016, at 05:27 , Romina Plitman <
[hidden email]> wrote:
>
> Hi all,
>
> I am relatively new to Imagej and I am trying to find the skeleton of a
> complex microvasculature.
>
> I manage to find the Skeleton and reduce noise using the features
> 'skeletonize' and 'Analize skeleton'. However, there is still some noise
> that I have to clean manually. To do so, I do a 3D projection of my
> skeleton (is easier to see the noise), manually select the noise and export
> their XY coordinates. I wrote a simple code in matlab that removes those
> pixels and I finally obtain my clean skeleton. The problem is that now I
> have a clean 3D projection, and to analyze the branches and junctions I
> need to go back to the 'normal' stack (the one before the 3D projection).
> Basically, I need to do the 3D projection in the opposite way.
>
> Is there something to do it in ImageJ? If not, can someone advice on how to
> achieve this?
>
> Many thanks!
> Romina
>
> --
> Romina Plitman Mayo
> PhD Student
> Centre for Trophoblast Research
> Department of Physiology, Development and Neuroscience & Department of
> Engineering
> University of Cambridge
> Cambridge, UK
>
> --
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