www.neuron.yale.edu

I constructed my neuron morphology linearly with connect statements, without explicitly setting locations in 3D or even 2D space. Now when I view the morphology using a Shape Plot, it appears that 2D coordinates have been automatically assigned to each compartment, leading to a strange spiral shape with overlapping sections that occlude each other. I would like to be able to use Shape Plot to generate some movies of voltage vs. time, but I would like to somehow linearize or stretch out the 2D representation of my 1.5D neuron so that it looks more like a 2D projection of a 3D neuron. Where is the code that is auto-generating the 2D coordinates, maybe I can hijack it and edit it with my own algorithm? Even better would be if I could click and drag each section in the GUI and just alter the angles of the visual representation on the Shape Plot, but that doesn't appear to be an option :(

aaronmil wrote:I constructed my neuron morphology linearly with connect statements, without explicitly setting locations in 3D or even 2D space. Now when I view the morphology using a Shape Plot, it appears that 2D coordinates have been automatically assigned to each compartment, leading to a strange spiral shape with overlapping sections that occlude each other.

Do it the right way and save yourself a lot of headaches--see the Programmers' Reference material on specification of geometry:
https://www.neuron.yale.edu/neuron/stat ... metry.html