Search found 9 matches
- Mon Apr 15, 2024 10:57 am
- Forum: Getting started
- Topic: Section-relative location of a segment
- Replies: 3
- Views: 838
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!
- Sat Apr 13, 2024 7:56 pm
- Forum: Getting started
- Topic: Section-relative location of a segment
- Replies: 3
- Views: 838
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 ...
- Sun Jan 28, 2024 8:28 am
- Forum: The GUI
- Topic: Somas not being positioned properly
- Replies: 7
- Views: 4233
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)...
- Fri Jan 26, 2024 9:36 am
- Forum: The GUI
- Topic: Somas not being positioned properly
- Replies: 7
- Views: 4233
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....
- Thu Jan 25, 2024 11:15 am
- Forum: The GUI
- Topic: Somas not being positioned properly
- Replies: 7
- Views: 4233
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...
- Wed Jan 24, 2024 2:26 pm
- Forum: The GUI
- Topic: Somas not being positioned properly
- Replies: 7
- Views: 4233
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...
- Tue Oct 03, 2023 4:15 am
- Forum: NEURON + Python
- Topic: Different total area from python and hoc cell class
- Replies: 5
- Views: 13365
Re: Different total area from python and hoc cell class
Thanks a lot, that cleared everything up nicely!
- Fri Sep 29, 2023 8:02 am
- Forum: NEURON + Python
- Topic: Different total area from python and hoc cell class
- Replies: 5
- Views: 13365
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.
2. I get the same results as before; 2022.6125052233679 is still the area using the python class.
- Thu Sep 28, 2023 6:23 am
- Forum: NEURON + Python
- Topic: Different total area from python and hoc cell class
- Replies: 5
- Views: 13365
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...