Hi all,
I have a set of 2d slices in xy plane at regular intervals in z-direction. I would like to re-contsruct this in 3d & obtain the coordinates (x,y,z). I have already segmented the objects in all 2d planes. I have to align the planes, such that, i obtain the objects to make a complete volume (voxel) & then obtain the centre of mass. I tried a few things, but its not working well enough. Does anyone have any suggestions?
Thank you!

Why are your slices misaligned?  If they came from something like a CT
or MRI instrument, they should be aligned, and, because the sample
most likely varies from slice to slice, your attempts to align them
again may mess up the alignment.

Anyway, to get the center of mass, you don't need the coordinates, you
only need to take your segmentation images (which are binary) as a 3D
image and run them through bwlabeln().  Then call regionprops, making
sure to pass in your original gray scale image.

ImageAnalyst <imageanalyst@mailinator.com> wrote in message <74f1acb5-724a-4170-9789-e0b3a3cd17f3@n3g2000yqb.googlegroups.com>...
> Why are your slices misaligned?  If they came from something like a CT
> or MRI instrument, they should be aligned, and, because the sample
> most likely varies from slice to slice, your attempts to align them
> again may mess up the alignment.
> 
> Anyway, to get the center of mass, you don't need the coordinates, you
> only need to take your segmentation images (which are binary) as a 3D
> image and run them through bwlabeln().  Then call regionprops, making
> sure to pass in your original gray scale image.

Hi there,
Thank you for the reply. My slices consist of nuclei of cells (labeled) in a developing embryo. So the nuclei change their position in x,y,z and t (time). I do go fast enough to capture the movement & my z resolution is high enough. However, the nuclei are many & also sometimes too close, sometimes fused, some dividing into two etc.. I segmented them in 2d , which works well. However, since I have to track their movement in 3d, i need to get the 3d reconstruction as right as possible.
Thanks!