I want to get a 3D surface model of a fossil hip bone with corrected taphonomic defects. However, there are larger cracks in the compact bone which I want to fill in order to obtain a smoother model (see the picture). In the slice, the outline can be well interpolated. I can do it manually, but I would like to know if there is some automatic way for example in ImageJ. I work in Avizo and I tried the Lasso tool with Auto trace edge, but it does not work very well. How would you proceed?
Dear Rebeka
I suggest that u use some image processing techniques for segmentation purposes, Using Matlab.. hope this can work
You could try to replace those darker pixels (say intensity value < 30) with a higher intensity value (say 125) which is similar to those on the border. You could also try more involved processes such as image segmentation for finding the cracked region and then perform image inpainting for filling the cracked region. All the best!
If you just want to close the crack and be able to reconstruct a closed surface from your CT by using some kind of Marching Cube algorithm, you could try the following.
You might have to smooth and reduce the resolution of your image to reduce the chances of the contours being stuck in bad local minimum but it should work.
This idea could be scripted using the Active Contour already implemented in ImageJ (see below):
http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:active_contour:start
https://en.wikipedia.org/wiki/Active_contour_model
Of course, if you only have this one specimen with 10-20 slices to segment correctly, this might not be worth the development but maybe it is more frequent than I think and more people could benefit from this kind of tool.
Good luck,
Bruno
If you only need to scan one hip bone, painting the gap(s) with white, followed by marching cubes, is the easiest way.
If however you need to scan many more hip bones of that species, you may consider creating a good surface of one scan (using the procedure above), and perform deformable surface registration on subsequent surfaces containing defects.
Unfortunately, I don't think ImageJ allows you to do this...
Good luck!
Depending on the purpose of the surface, too. I suppose manually correcting the surface in 3D modeling software will be easier and faster then masking or contour interpolating during the segmentation process. You can use CT slice as an image background to reconstruct the surface properly. Even though not automatic I guess this should be fast and adequate enough.
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