Search found 9 matches

by opdalex
Mon Apr 15, 2024 10:57 am
Forum: Getting started
Topic: Section-relative location of a segment
Replies: 3
Views: 1229

Re: Section-relative location of a segment

I am a bit embarassed to recognize that I have definitely used this before. Thanks for digging this up!
by opdalex
Sat Apr 13, 2024 7:56 pm
Forum: Getting started
Topic: Section-relative location of a segment
Replies: 3
Views: 1229

Section-relative location of a segment

Hi. I have not been able to find a simple, pythonic way of extracting the section-relative location of a segment. I find it quite surprising that I have not found it considering the location is available from the segment object's string representation. Good thing that it is, because that is what my ...
by opdalex
Sun Jan 28, 2024 8:28 am
Forum: The GUI
Topic: Somas not being positioned properly
Replies: 7
Views: 4474

Re: Somas not being positioned properly

The alternative method you described worked well, the cells are positioned as I intended without any off-set somas. I replaced _set_position with this function: def set_position(self, x, y, z): soma = self.soma[0] root = soma.wholetree()[0] for i in range(root.n3d()): root.pt3dchange(i, (x - self.x)...
by opdalex
Fri Jan 26, 2024 9:36 am
Forum: The GUI
Topic: Somas not being positioned properly
Replies: 7
Views: 4474

Re: Somas not being positioned properly

You are right, of course, this piece of code is not written in the best manner. Sorry if it was a source of confusion. Possibly related to the issue, I am using Windows 11, python 3.9.16 and NEURON 8.2.0. I saw a similar set of circumstances in this post: https://www.neuron.yale.edu/phpBB/viewtopic....
by opdalex
Thu Jan 25, 2024 11:15 am
Forum: The GUI
Topic: Somas not being positioned properly
Replies: 7
Views: 4474

Re: Somas not being positioned properly

I have to state that this mapping is as intended, and of little functional importance. Since the question came up, however, some things are needed to explain this unintuitive x, y -> x, z mapping. First of all, the cell morphology I am using is positioned such that the soma is above the dendritic tr...
by opdalex
Wed Jan 24, 2024 2:26 pm
Forum: The GUI
Topic: Somas not being positioned properly
Replies: 7
Views: 4474

Somas not being positioned properly

Hi! I am attempting to place a grid of cells, all duplicates from one neurolucida morphology, in a shapeplot in NEURON. My issue is that the somas do not move in synchronization with their dendritic trees when I use the "_set_position" function from the Ball-and-stick tutorial (link: https...
by opdalex
Tue Oct 03, 2023 4:15 am
Forum: NEURON + Python
Topic: Different total area from python and hoc cell class
Replies: 5
Views: 14886

Re: Different total area from python and hoc cell class

Thanks a lot, that cleared everything up nicely!
by opdalex
Fri Sep 29, 2023 8:02 am
Forum: NEURON + Python
Topic: Different total area from python and hoc cell class
Replies: 5
Views: 14886

Re: Different total area from python and hoc cell class

1. I am using NEURON version 8.0.0 (compatibility with both python 2 and 3 is preferred to newest version)
2. I get the same results as before; 2022.6125052233679 is still the area using the python class.
by opdalex
Thu Sep 28, 2023 6:23 am
Forum: NEURON + Python
Topic: Different total area from python and hoc cell class
Replies: 5
Views: 14886

Different total area from python and hoc cell class

Hi, I have stumbled upon an issue with different measures of total area when trying to convert an old method to using a python class to represent a neuron. The old method uses the NEURON gui; from there using import 3d for importing a Neurolucida reconstruction, then exporting to CellBuilder to edit...