Shape Plots for 1.5D Neurons

Using the graphical user interface to build and exercise models. Includes customizing the GUI by writing a little bit of hoc.
Post Reply
aaronmil
Posts: 33
Joined: Fri Apr 25, 2014 10:54 am

Shape Plots for 1.5D Neurons

Post by aaronmil » Thu Sep 24, 2015 10:57 am

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 :(

ted
Site Admin
Posts: 5306
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: Shape Plots for 1.5D Neurons

Post by ted » Thu Sep 24, 2015 11:08 am

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

Post Reply