From 3D Projection back to stack

Posted by Romina Plitman on Aug 04, 2016; 9:27am
URL: http://imagej.273.s1.nabble.com/From-3D-Projection-back-to-stack-tp5016974.html

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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