This is an interesting case. I followed muratmaga’s advice on rescaling the intensity and casting to uint16. By doing this the 49.1 GiB set of 2,129 TIFF files (17.6 GiB zipped) was able to be saved from 3D Slicer as a single 24.7 GiB file.
However I am not sure that there is any problem with the specimen or its positioning.
From the 3D rendering the scan indeed looks to me like a long bird’s beak and the front half of its head, more-or-less centred within a cylinder. Seeing a cylinder generated from a CT scan makes sense to me. What seems slightly odd to me is that the cylinder axis doesn’t quite line up with the image coordinate system (evident from the bounding box, represented as the ROI below).
10800 rescaled units & up (perspective 3D rendering)
10800 rescaled units & up (orthographic 3D rendering)
11200 rescaled units & up (perspective 3D rendering)
So I wonder whether the original CT scan data may have been resampled into a new coordinate system. (Perhaps that also explains the intensity scaling in the range of 0 to 1 for the TIFF files.)
Based on the ability to get some sensible 3D rendering, I’m not sure that the background poses such a problem. The suggestion that “the contrast between the bird and the surrounding area is limited” may be a matter of ‘perspective’. That is, if the window is judiciously chosen, then the contrast looks better. It might be easier to specify appropriate settings once the above intensity rescaling has been done.
Do you want just the beak, or the flesh and skin and feathers too?
—DIV
P.S. Here are the contents of the *.VP file containing my 3D rendering settings for the rescaled intensities.
1
1
1
0.2
0
1
8 -1000 0 11200 0 19000 0.8 83849.5625 1
4 0 1 985.12 1
20 10000 0.3 0.3 1 15000 0.3 1 0.3 22000 1 0 0 49014.53515625 1 0.912535 0.0374849 61858.734375 1 0.3 0.3
P.P.S. There is a kind of limitation in 3D Slicer that will prevent a user from entering an intensity value in the opacity or colour mapping that’s above some nominal ‘maximum’ by directly typing it in. (Some people might call this a bug.) The workarounds are to either drag the rightmost grey circular knob to the far right, or to manually edit the VP file. It’s not very convenient.