Problem setting thickness on my stack

hi again. I’m working with a stack of 160nm thickness, wich after some calculations amounts to 9.38pixels.

now, when I set the thickness of my z-stack in TrakEM2 and try to do a 3d viewing of the areas I marked, what I get is this:

Snapshot.tif (2.2 MB)

where either the thickness is doubled to each side or the distance between layers is halved. aniway, the problem is they overlap, and when I go to set z-layer and thickness it only allows me to set a scale, but not change them individually.

someone knows what I’m doing wrong?

Thanks for your time


I really don’t use TrackEM2 often enough myself to be of much help… but perhaps @bogovicj can help?

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Hi @meperegri,

What I think may be happening is that your values for z-thickness is clashing with your z-spacing,
but I can’t know for sure unless you provide a little more information.

In the trakem2 window, there’s a layers tab with all your z sections, if you right-click on one, you’ll see something like this:

Can you take a screenshot like this so we can see what you have?

Notice that in my case, the z-layers are separated by “1”, and the thickness is “1”.
If I increase the thickness without changing their positions, then the slices will overlap.
Suppose I change the thickness values of every layer to “2”, then I’d have to set the values of z to be:
0, 2, 4, 6, …
in order to avoid overlap.

Hope that helps, but if this is not the problem, then the more information you provide, the better chance we’ll be able to help :slight_smile:

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hi! sorry for the delay @bogovicj

This looks correct (the number is weird because I had to translate to nanometers). It autospaced all the layers the desired amount (those 9&something pixels, aka 160nm)

sorry to refloat this, but I’ve kept searching for solutions, and even setting the thickness to 1 and the z level to increments of 10 I get this:

It really is a problem because it hides quite a llot of information.

thanks for your time