When viewing an image stack in 3D, what is the correlation between the Z-thickness increments and the distance between each slice? i.e. if i scanned 1 slice every 10 micrometers, what z-thickness value would accurately portray this distance between each slice?

Also, furthermore, what do you think is the ideal distance between slices/magnification for the purpose of trying to reconstruct neuronal pathways in the drosophila brain? The project I'm working on now would be greatly benefitted by the work being done by the Fly brain atlas project being done at Janelia Farms, and if possible, I'd like to make my work consistent with the standards being employed there.

Thanks!

The "theoretical" best z-thickness should be the ratio of z-step-size divided by the xy-plan step-size. For example, if in your image, the xy plane resolution is 0.6um, and z step size is 2um, then you should input 2/0.6=3.33 there. This basically will give an isotropic view.

However, V3D was designed to make it flexible for different viewing modes, such as a user wants to use different z-thickness.

Also note that you may want to turn off the "compression" of your video card (the button close to "z-thckness" in the 3d viewer), if the rendered quality is more important.

For neruon tracing, the z-thickness is automatically used as a weighting factor in V3D-Neuron tracing. Typically we just make each voxel isotropic, thus the above-mentioned method to choose z-thickness should be used in that case.