Search found 5961 matches

by ted
Tue Oct 19, 2021 12:43 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: undersampling curves
Replies: 9
Views: 177

Re: undersampling curves

This note is primarily for others who may read this thread. Using NMODL for "data processing on the fly" raises several potential issues. 1. In this particular application, the sequence of execution of NMODL-specified mechanisms is important. Clearly all mechanisms that WRITE ica must be e...
by ted
Wed Oct 13, 2021 1:05 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: undersampling curves
Replies: 9
Views: 177

Re: undersampling curves

I begin to see your problem. I thought you were working with some generic optimization library that you could just feed some postprocessed data after a simulation was complete. Instead, you're probably using

Code: Select all

xopen("fit.ses")
to recreate a Multiple Run Fitter, right?
by ted
Wed Oct 13, 2021 12:37 pm
Forum: NEURON + Python
Topic: Error running NEURON with embedded Python
Replies: 3
Views: 2422

Re: Error running NEURON with embedded Python

Thanks for following up with the fix for that!
by ted
Wed Oct 13, 2021 12:13 pm
Forum: NEURON + Python
Topic: How to set spike detection threshold for pc.spike_record
Replies: 2
Views: 63

Re: How to set spike detection threshold for pc.spike_record

netconExc in the 2005 post is the name of a user-created variable. It has nothing to do with the question you asked. ParallelContext.threshold() is what you want. Read about it in the Programmer's Reference in the documentation of the ParallelContext class https://nrn.readthedocs.io/en/latest/python...
by ted
Fri Oct 08, 2021 12:10 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: undersampling curves
Replies: 9
Views: 177

Re: undersampling curves

Thanks for the explanation. Please excuse me if the following discussion seems rather basic, but we try to be mindful of the fact that not everyone who reads these comments will have the same level of expertise. I am also not sure if I should be doing this calculation in my main hoc or in a mod file...
by ted
Thu Oct 07, 2021 11:31 am
Forum: Adding new mechanisms and functions to NEURON
Topic: undersampling curves
Replies: 9
Views: 177

Re: undersampling curves

A good question about a common practical issue. In order to provide the most appropriate answer, I'll need a bit more information. I have experimental traces of Ca fluorescent imaging that are sampled at 0.5 ms. I want to fit these recordings with my model but to do that I need to undersample the si...
by ted
Fri Sep 24, 2021 10:19 am
Forum: NEURON + Python
Topic: Problem plotting PlotShape
Replies: 5
Views: 178

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: 96

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: 178

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: 155

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: 158

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: 158

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: 155

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: 155

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: 103

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).