Scaling

[Mike]

Hi,

I'm trying to understand where in neuromantic I can set the X,Y and Z
scales, that is to say how do I set the distance in microns between
each stack and number of pixles corresponding to a certain length in x
and y.

Many thanks,
Mike

[Ben Suter]

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/

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

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[Mike Vella]

Thanks Ben,

I actually found the neuromantic way of scaling slightly easier than
using the neuronland stuff (neuronland software wants me to set
windows PATH variable etc, which seems an unecessary complication) so
I'll stick to that for the time being.

All the best,
Mike

[oren A]

Did you managed to find how to set the scale?

Thank You.