How to set Voxel Size?

[oren A]

Hello,

I do not found where to set the voxel size? How do Neuromantic know what size the picture is?

Thank You,

Oren.

[oren A]

Anyone?

[Ben Suter]

Hi Oren,

I recommend that you avoid setting the scale withing Neuromantic. The
default assumption is that all voxels are 1x1x1, and the measurements
in the resulting SWC files are interpreted as being in micrometers.

In my own work, I reconstruct the entire neuron in Neuromantic without
adjusting the scale. When I'm done, I use a different program to
adjust the X, Y, Z axis scales, and optionally the diameters, and
sometimes I shift the soma to the origin, etc.

I do most of this in Matlab using custom routines, but the freely
available NeuronLand converter software can do this too (see the
command options in the manual under the "Global Positioning" heading):
http://neuronland.org/

That said, if you wish to "transform" your reconstruction in
Neuromantic, then the relevant commands can be found under: Tree
Processing -> Transformations -> Scale Tree

Again, I recommend that you only apply those transformations when
you've completed the reconstruction.

I'm not involved in developing Neuromantic, so take my advice with a
grain of salt.

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[Ben Suter]

Please also have a look through the older threads, as this
question/topic has been discussed frequently in the past. One
particular post of interest, from the developer:

https://groups.google.com/d/msg/neuromanticusergroup/njTuFch0khs/W5FPM3nBb0oJ