Search found 5653 matches

by ted
Thu Dec 12, 2019 10:49 am
Forum: Anatomically detailed models
Topic: Precise 3D morphology
Replies: 6
Views: 34

Re: Precise 3D morphology

it seems to be very precise What seems to be very precise? Spine location, detailed shape of spine heads, what? The people at MicroBrightField are very helpful. Address questions about Neurolucida to them and they'll be glad to tell you what you want to know. Or search the Internet for neurolucida ...
by ted
Wed Dec 11, 2019 11:05 am
Forum: Anatomically detailed models
Topic: Precise 3D morphology
Replies: 6
Views: 34

Re: Precise 3D morphology

Fine spatial detail doesn't matter much for electrical signals, which have length constants on the order of tens or hundreds of microns. It can be important for chemical signals, especially intracellular calcium and second messengers, not to mention ions and neurotransmitters in tissue extracellular...
by ted
Wed Dec 11, 2019 12:00 am
Forum: Anatomically detailed models
Topic: Precise 3D morphology
Replies: 6
Views: 34

Re: Precise 3D morphology

SWC Plus doesn't really seem to exist. Its github site shows one contributor and three commits, the last commit being in 2016. Has there been a single publication about SWC Plus, ever? Who uses the SWC Plus format? Are there any tools that generate or read SWC Plus files? Are there any morphometric ...
by ted
Mon Dec 09, 2019 1:01 pm
Forum: Hot tips
Topic: Extracellular stimulation and recording
Replies: 4
Views: 22137

Re: Extracellular stimulation and recording

LFPsimpy is a welcome addition to the tools that can be used to calculate extracellular potentials generated by the activity of model neurons! Note to others who may read this thread: LFPsim and LFPsimpy implement calculation of extracellular potentials generated by activity of model neurons. Neithe...
by ted
Mon Dec 09, 2019 12:55 pm
Forum: Getting started
Topic: construct a single myelinated axon
Replies: 10
Views: 518

Re: construct a single myelinated axon

Axon Diameter(internal) is 10um, and the myelin thickness is 2um, I wonder why for the myelin section, the diameter was set to be 10um instead of 12um.
Internal diameter controls the axial resistance of the axon (resistance to current flow down the length of the axon).
by ted
Fri Dec 06, 2019 11:26 am
Forum: Other tools
Topic: Allen Institute Brain Modeling Tool Kit (BMTK) + Gap Junctions
Replies: 1
Views: 195

Re: Allen Institute Brain Modeling Tool Kit (BMTK) + Gap Junctions

First, just to help isolate the cause of the problem-- NOT using BMTK 1. have you successfully implemented and executed simulations of a toy network model that involves gap junctions and is NOT parallelized? 2. have you successfully implemented and executed simulations of the same network model, but...
by ted
Thu Dec 05, 2019 11:21 pm
Forum: Reaction-diffusion in NEURON
Topic: The equilibrium between the FS and external
Replies: 20
Views: 703

Re: The equilibrium between the FS and external

Any one can help me to find the math behind extracellular mechanism please? The topic of this thread is "The equilibrium between the FS and external," as clarified in your first post in this thread. That has nothing to do with the extracellular mechanism, as you will discover if you read the Progra...
by ted
Wed Dec 04, 2019 10:37 am
Forum: NEURON + Python
Topic: How to access HOC arrays from Python?
Replies: 2
Views: 56

Re: How to access HOC arrays from Python?

The hoc notation sectionname [ i ] does not really mean that there is an "array" of sections. Instead, treat the [ i ] as part of the section's name. Except for the very simplest cases (no more than half a dozen sections or so) It is probably more effort than it is worth to re-implement a hoc-specif...
by ted
Tue Dec 03, 2019 11:01 am
Forum: The GUI
Topic: GUI RunControl panel and Window size
Replies: 1
Views: 47

Re: GUI RunControl panel and Window size

How can I start RunControl panel from Python to avoid clicking each time on Tools->RunControl If you already see the NEURON Main Menu toolbar, h.nrncontrolmenu() How did I figure this out? NEURON's standard run system and much of its GUI interface are defined by code in nrn/share/nrn/lib/hoc If you...
by ted
Tue Dec 03, 2019 10:36 am
Forum: The GUI
Topic: GUI 2 with Python
Replies: 1
Views: 37

Re: GUI 2 with Python

Worthy goals abound. All things are possible through programming. Anyone who has the interest, expertise, and time is welcome to pitch in.
by ted
Mon Dec 02, 2019 3:21 pm
Forum: NEURON + Python
Topic: Shape plot update from Python
Replies: 2
Views: 51

Re: Shape plot update from Python

I would like to monitor "cai" variable across shape plot. After I execute this code it shows correctly what I want to monitor, except that it wont update . . . When I specify the same parameters with mouse - it works and the plot is updates. The Programmer's Reference documentation of PlotShape sho...
by ted
Mon Dec 02, 2019 12:09 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Accessing state variables of one mechanisn in another mechanism
Replies: 1
Views: 54

Re: Accessing state variables of one mechanisn in another mechanism

One way would be to make the dependent mechanisms' cAMP variables be POINTERs. Read about setpointer in the Programmer's Reference. For an example, see caL.mod and kir2.mod in ModelDB entry 39949. These mechanisms specify ion channels whose properties are modulated by a second messenger, the concent...
by ted
Sun Dec 01, 2019 11:37 am
Forum: Adding new mechanisms and functions to NEURON
Topic: where to declare cai and cao ?
Replies: 1
Views: 65

Re: where to declare cai and cao ?

At least in two modules for low and high threshold calcium currents read inner and outer calcium concentrations (cai, cao) and compute the GHK equation. Yes, but neither of those NMODL-specified mechanisms WRITEs cai or cao, so their assignment statements cai = something cao = something else do not...
by ted
Tue Nov 26, 2019 4:36 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: using diam and L params inside MODL file
Replies: 5
Views: 272

Re: using diam and L params inside MODL file

Models of diffusion can be implemented with NMODL, but NMODL is best suited for nearly cylindrical geometries--structures in which diameter changes very slowly along the length of a neurite--and under conditions in which concentration gradients and solute fluxes are either predominantly longitudinal...
by ted
Tue Nov 26, 2019 2:53 pm
Forum: NEURON + Python
Topic: How to get synapse offset/position
Replies: 5
Views: 150

Re: How to get synapse offset/position

Good. I hope you're still in an educational mood. The d_lambda rule is a rational basis for specifying the spatial discretization of a model. It involves setting nseg to a value that is a small fraction of the AC length constant at a high frequency. The rationale behind it is developed in the second...