Z-stack setup

[Alexander V. Kalachev-2]

Dear ImageJ users,

can anyone provide me with a way how to correctly setup a Z-stack in order to make a 3D
reconstruction with TrackEM2 plugin? For my work I need to make a series of sections from a
material embedded into Araldite-Epon resin. I have a series of 1.5 micrometers thick sections
with a spacing between sections of 3 micrometers. How to correctly set these parameters in ImageJ?

With kind regards,
Alexander

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[Saalfeld, Stephan]

You would set the voxel depth to 4.5um.  ImageJ does not distinguish
spacing and thickness.  The easiest way to import this stack into
TrakEM2 is to save it as a series of 2D images.

Side note: For 3D reconstruction, I was never happy to hear of thin
sections with extra-spacing.  This way, you are willingly undersampling
the axial dimension.  I.e. while you get excellent detail in the plane,
the continuity of your signal along z is anecdotal.  It's like scanning
a confocal image at very low resolution with a super small pinhole.
 Nobody would do that.

Best,
Stephan

On Wed, 2017-07-12 at 16:02 +1000, Alexander V. Kalachev wrote:

> Dear ImageJ users,
>
> can anyone provide me with a way how to correctly setup a Z-stack in
> order to make a 3D
> reconstruction with TrackEM2 plugin? For my work I need to make a
> series of sections from a
> material embedded into Araldite-Epon resin. I have a series of 1.5
> micrometers thick sections
> with a spacing between sections of 3 micrometers. How to correctly
> set these parameters in ImageJ?
>
> With kind regards,
> Alexander
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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