http://imagej.273.s1.nabble.com/From-3D-Projection-back-to-stack-tp5016974p5017002.html
Thanks for the responses and ideas. I manage to find the pixel coordinates
> Hi Ignacio, Herbie, Gabriel, Niko and Kenneth,
>
> Thanks for the responses and ideas. I manage to find the pixel coordinates
> in the skeleton file of the noise and wrote a simple matlab code to erase
> it.
>
> Thanks again for the help!
>
> Romina
>
> On Fri, Aug 5, 2016 at 1:42 PM, Kenneth Sloan <
[hidden email]>
> wrote:
>
>> 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
>> >
>> > --
>> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>
>
>
> --
> Romina Plitman Mayo
> PhD Student
> Centre for Trophoblast Research, Department of Physiology, Development and
> Neuroscience
> Nanoscience Centre, Department of Engineering
> University of Cambridge
> Cambridge, UK
>