Z-stack setup

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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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Re: Z-stack setup

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
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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