Search found 5955 matches

by ted
Fri Sep 24, 2021 10:19 am
Forum: NEURON + Python
Topic: Problem plotting PlotShape
Replies: 5
Views: 55

Re: Problem plotting PlotShape

Or maybe the problem is with matplotlib. Can you try an earlier Python under MSWin?
by ted
Thu Sep 23, 2021 11:41 am
Forum: Hot tips
Topic: fix "unable to open font"
Replies: 0
Views: 20

fix "unable to open font"

If you're getting messages like
unable to open font "*helvetica-medium-r-normal*--14*", using "fixed"
do this for Debian-related Linux distributions:

sudo apt-get install xfonts-100dpi
then log out and log back in.

For RedHat-related distributions, install xorg-x11-fonts-100dpi
by ted
Thu Sep 23, 2021 11:30 am
Forum: NEURON + Python
Topic: Problem plotting PlotShape
Replies: 5
Views: 55

Re: Problem plotting PlotShape

Works for me under CentOS 7 with Python 3.6.8 and NEURON 8.0a-575-gd9462cc master (d9462cc) 2021-05-27 (installed from source code). Also works under Mint 20.1 with Python 3.8 and NEURON 8.0.0 HEAD (429d11ef) 2021-04-30 (installed via pip). That said, both cases generated a MatplotlibDeprecationWarn...
by ted
Tue Sep 21, 2021 5:25 pm
Forum: Anatomically detailed models
Topic: Importing Imaris files using import 3D tool
Replies: 3
Views: 68

Re: Importing Imaris files using import 3D tool

This article mentions several approaches to semiautomatic morphological construction, and contains a detailed, step-by-step description of a workflow for semiautomatic morphological reconstruction (using freely available software developed in our laboratory) : @InCollection{WOS:000635353100010, auth...
by ted
Sun Sep 19, 2021 1:25 am
Forum: NEURON + Python
Topic: problem instantiating a hoc template from python
Replies: 3
Views: 74

Re: problem instantiating a hoc template from python

I am using a script of yours Actually, no, you're not. The comment says Based on code by Ted Carnevale but that doesn't mean the code is a replication in python of anything that I wrote. One key difference is that this python code uses piecewise one-dimensional cubic interpolation to calculate the ...
by ted
Sat Sep 18, 2021 1:08 am
Forum: NEURON + Python
Topic: problem instantiating a hoc template from python
Replies: 3
Views: 74

Re: problem instantiating a hoc template from python

Looks like the template's proc init expects three arguments. The first would be a cell-instance-specific gid, the second looks like a parameter that is ultimately used to associate each cell with its own particular pseudorandom sequence, and the third has something to do with setting up synaptic mec...
by ted
Sat Sep 18, 2021 1:02 am
Forum: Anatomically detailed models
Topic: Error in loading morphology from swc file
Replies: 4
Views: 62

Re: Error in loading morphology from swc file

Truly a mystery wrapped in an enigma. A cautionary note: The MSN class definition contains the statement h.celsius = 35 It may well be that the MSN class involves one or more mechanisms that assume an operating temperature of 35 deg C, but unfortunately h.celsius is a global variable. What do you th...
by ted
Fri Sep 17, 2021 11:53 am
Forum: Anatomically detailed models
Topic: Error in loading morphology from swc file
Replies: 4
Views: 62

Re: Error in loading morphology from swc file

trying to run already existing code. While loading a morphology of a spiny projection neuron I get the following error Very strange. The Import3d GUI tool had no problem with this swc file under Linux Mint 20.1 (NEURON 8.0.0 HEAD (429d11ef) 2021-04-30 installed yesterday via pip3) or CentOS 7 with ...
by ted
Fri Sep 17, 2021 9:59 am
Forum: Anatomically detailed models
Topic: cable model with manual diameters and dynamics
Replies: 1
Views: 39

Re: cable model with manual diameters and dynamics

Can't answer your questions. The code excerpt contains no statement that creates a section or references the properties of a section or segment. There isn't even a reference to any NEURON-specific keyword (pi and names of common units like siemens and um don't count).
by ted
Fri Sep 17, 2021 9:50 am
Forum: NEURON + Python
Topic: undefined symbol: nrnpython_start
Replies: 8
Views: 137

Re: undefined symbol: nrnpython_start

After installing NEURON with pip3 install neuron I didn't add it to the path. At trying to compile mod files Ubuntu prompts me to install neuron-dev with sudo apt which was version 7.6.3. How (not) helpful. Under Linux Mint (a close cousin of Ubuntu), pip install of NEURON simply adds .local/bin to...
by ted
Wed Sep 15, 2021 2:16 pm
Forum: NEURON + Python
Topic: undefined symbol: nrnpython_start
Replies: 8
Views: 137

Re: undefined symbol: nrnpython_start

The output with a path with no spaces is the same as the one above Right, but did NEURON still crash? I just re-read your message from earlier today and realized the meaning of these sentences: I notice that the NEURON version is 7.6.3, even though on NEURON's website 8.0 is the latest version. If ...
by ted
Wed Sep 15, 2021 11:33 am
Forum: NEURON + Python
Topic: undefined symbol: nrnpython_start
Replies: 8
Views: 137

Re: undefined symbol: nrnpython_start

Thanks for your prompt response, but that's not "the entire message that NEURON prints to the terminal". The most important missing item is the first line, which reports details about the version of NEURON that you're using--just in case you're running into a bug that has already been fixe...
by ted
Tue Sep 14, 2021 11:37 am
Forum: NEURON + Python
Topic: undefined symbol: nrnpython_start
Replies: 8
Views: 137

Re: undefined symbol: nrnpython_start

Even if I have the mod files in the same level of the directory tree as the rest of the code . . . Please do this test. Create a new directory. Put your mod files in that directory. In that directory execute nrnivmodl Then in that same directory execute nrngui What is the entire message that NEURON...
by ted
Tue Sep 14, 2021 11:32 am
Forum: Anatomically detailed models
Topic: Importing Imaris files using import 3D tool
Replies: 3
Views: 68

Re: Importing Imaris files using import 3D tool

I tried to look for a way to convert the Imaris files to SWC but could not find any good options. Import3d's algorithms require an input file that contains morphometric data, specifically measurements of diameters at particular locations in space, structured in a way that identifies neurites and br...
by ted
Fri Sep 10, 2021 10:58 am
Forum: Other questions
Topic: List of all currents that comprise segment membrane current
Replies: 1
Views: 64

Re: List of all currents that comprise segment membrane current

I cannot seem to get the sum of the ionic currents for each segment to equal the segment's i_membrane_
How big is the discrepancy? If you are using fixed time step, does the discrepancy become smaller if you switch to adaptive integration?