If you're opening the Zeiss file then the scaling should be correct, but to
double-check press Ctrl (or Command on a Mac)-Shift-P. Check that the pixel
height, width, and depth are what they should be.
If you used an air lens without Refractive Index Correction in the
software, that will flatten your volume relative to reality but it wouldn't
turn a sphere into a sheet.
If you do an Ortho view (Ctrl-Shift-H) does it look like the right height?
If it looks flat then it's not a problem with the 3D viewer but somewhere
else.
Maybe your specimen is a lot flatter than you think?
-Esteban
On May 23, 2016 1:33 PM, "Xi Chen" <
[hidden email]> wrote:
> Hi friends,
>
> I tried to use imageJ to build up 3D construction from my stack images
> generated by zeiss lsm 780. The samples used for imaging are mouse brain
> sections. But after followed the instruction using the default setting, I
> got a very thin layer for the neuron cells which should be nearly sphere.
>
> I don't know if this is true refection of my samples or there are some
> mistakes I made. Does anybody have any suggestion for this? Thanks in
> advance!
>
> Best,
>
> Xi
>
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