Understainding how 3D viewer works

Posted by Eugeniu Nacu on
URL: http://imagej.273.s1.nabble.com/Understainding-how-3D-viewer-works-tp4999802.html

Hi everyone,

I am acquiring Z-stacks with the Zeiss LSM780 to acquire confocal
images, and I save them in the LSM5 format. I want to reconstruct the
stacks into a 3D image.

Since I am new to using the 3D viewer and I was wondering if someone
could explain how the 3D viewer actually works. I am interested in
knowing what metadata is used and what actually is going on when the 3D
image is created.

Also, I was wondering if you could give me advice on the following issue:
I have an undersampled sample such as the following: it is a 483.03µm
thick z-stack, with 10 z-slices, z-slice thickness of 2µm, and z-step of
53.67µm.
I want to create a 3D view of this sample where my 2µm z-slices would be
rougly 53.67µm apart.
Right now it seems that the Fiji just uses the z-step of 53.67µm as the
voxel depth instead of 2µm. Also it seems to not know the difference
between voxel depth and z-step because when I change the voxel depth to
2µm the 3D viewer "squashes" the image into 20µm by simply layering the
different z-slices on top of each other.
Any idea how to make the 3D viewer read the correct voxel depth and the
z-step so that it can spread my z-slices accordingly in the 3D image?

Thanks a lot!
Eugen

--
Dr. Eugeniu Nacu

Postdoctoral Fellow in Group of Prof. Dr. Elly Tanaka
Center for Regenerative Therapies Dresden

Fetscherstr 105, 01307 Dresden, Germany

Tel: [phone]
Fax: [phone]

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