Understainding how 3D viewer works

[Eugeniu Nacu]

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]

--------------------------------

I am currently trying to reduce the number of times I check my email per day in order to avoid distractions and increase productivity.
Therefore my response to your emails may be somewhat slow.

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[Benjamin Schmid-2]

Hi,

On 22:03 Thu 16 Aug     , Eugeniu Nacu wrote:

> 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

... [show rest of quote]

The 3D Viewer indeed assumes that the z-step equals the slice thickness.
It reads this information from the image calibration, which can manually
be adjusted under -Image-Properties. Unfortunately, there's no way to
specify the z-step there, so no chance for the 3D Viewer to get that
info.

For a quick solution which doesn't require any programming, you could just
fill your stack with empty slices. I can also implement some function to
separate slices in x-, y- and z-dimensions in the 3D Viewer. However it
might take a few days before it's done.

Volume renderings in the 3D Viewer are done in the following way:
For each plane, a rectangle is created which gets a texture applied
(namely that particular plane). The distance between rectangles is the
voxel depth. Rectangles are created in x-, y- and z- direction, however
only one set is visible a time, depending on the view orientation.

>
> --
> 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]

Hey, you are just next door, I'm at the MPI-CBG, so we could also meet
if you want.
>
> I am currently trying to reduce the number of times I check my email per day in order to avoid distractions and increase productivity.
> Therefore my response to your emails may be somewhat slow.
>
me too ;)

Cheers,
Bene

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