Search found 55 matches

by alexandrapierri
Wed Jan 04, 2023 7:32 pm
Forum: Anatomically detailed models
Topic: SWC file content
Replies: 6
Views: 143

Re: SWC file content

good to know, thanks that's very interesting.
I relied on this link if others seek similar information.

http://www.neuronland.org/NLMorphologyC ... /Spec.html
by alexandrapierri
Tue Jan 03, 2023 3:13 pm
Forum: Anatomically detailed models
Topic: SWC file content
Replies: 6
Views: 143

Re: SWC file content

thank you that makes sense, I thought I should've looked in Programmer's reference.
by alexandrapierri
Mon Jan 02, 2023 5:24 pm
Forum: Anatomically detailed models
Topic: SWC file content
Replies: 6
Views: 143

SWC file content

Hello

I am looking for documentation on the swc morphology format.
I want to be reminded of what each of the columns in a given file represents.

thank you,
Alexandra
by alexandrapierri
Fri Dec 09, 2022 6:41 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: alternating the expression of GABA current in mod file
Replies: 5
Views: 251

Re: alternating the expression of GABA current in mod file

Hello Ted this is again within the context of Depolarization induced suppression of inhibition (DSI). I am implementing a simpler model this time. I want the DSI to start after the pyramidal cell is depolarized and last for 1.8 seconds. I want the amplitude of the current to decay according to the f...
by alexandrapierri
Wed Dec 07, 2022 9:06 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: alternating the expression of GABA current in mod file
Replies: 5
Views: 251

alternating the expression of GABA current in mod file

Hello I have a question related to NMODL syntax. I would like the expression for the GABA current to change at the onset of a patch clamp simulation. The patch clamp is not defined in the NMODL file but in my python script. In the mod file, I have set that if my voltage goes beyond a certain value, ...
by alexandrapierri
Fri Dec 02, 2022 12:09 am
Forum: NEURON + Python
Topic: Switching L2/3 morphology in model but preserving intrinsic and synaptic properties.
Replies: 2
Views: 112

Switching L2/3 morphology in model but preserving intrinsic and synaptic properties.

Hello I am using the following model by Aberra 2018 (https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=241165). I would like to replace the L23 morphology file with my own morphology file but preserve the synaptic distribution and intrinsic properties of the cell. If I simply replace the ...
by alexandrapierri
Tue Nov 15, 2022 8:32 pm
Forum: NEURON + Python
Topic: recording delivered pulses using pulsedistrib.zip
Replies: 3
Views: 134

Re: recording delivered pulses using pulsedistrib.zip

thank you Ted, First I would like to say that the syntax: "h.ipulse2(bs.soma(0.5))" gives error "hoc object doesn't have attribute ipulse2" which tells me that I am using the wrong syntax. Should I use "insert" or a different syntax to deliver the pulses to the basket c...
by alexandrapierri
Tue Nov 15, 2022 12:18 am
Forum: NEURON + Python
Topic: recording delivered pulses using pulsedistrib.zip
Replies: 3
Views: 134

recording delivered pulses using pulsedistrib.zip

Hello I am using pulsedistrib.zip, to deliver a set of 10 pulses of 1ms approx per pulse. I am having difficulty controlling the Ipulse2 parameters either from my python script or directly from within the mod file. For example, the following syntax doesn't work: iclamp = h.Ipulse2(bs.soma(0.5)) #whe...
by alexandrapierri
Tue Nov 08, 2022 10:48 pm
Forum: NEURON + Python
Topic: Depolarization step during voltage clamp
Replies: 4
Views: 156

Re: Depolarization step during voltage clamp

Yes, this fixes the problem. :)

Thank you!
by alexandrapierri
Thu Nov 03, 2022 10:35 pm
Forum: NEURON + Python
Topic: record calcium concentration only from pyramidal cells
Replies: 2
Views: 186

Re: record calcium concentration only from pyramidal cells

thank you Ted, I responded with a private message attaching my mod file.
by alexandrapierri
Tue Nov 01, 2022 7:49 pm
Forum: NEURON + Python
Topic: Depolarization step during voltage clamp
Replies: 4
Views: 156

Re: Depolarization step during voltage clamp

thank you Ted this works great except that I am facing now an issue holding the potential to the exact voltage defined by the SEClamp. Here are two examples: in the first case the voltage is held at -70 for 1000ms (but in praxis there are transients and the voltage deviates from -70mV) and in the se...
by alexandrapierri
Mon Oct 31, 2022 9:56 pm
Forum: NEURON + Python
Topic: Depolarization step during voltage clamp
Replies: 4
Views: 156

Depolarization step during voltage clamp

Hello I am trying to do the trivial task of adding a depolarization step during pyramidal cell voltage clamp. The holding potential is at -70mV and after some time I want to depolarize the cell to 0mV for 200ms. I treat this as two separate voltage clamps. However, the following syntax yields a volt...
by alexandrapierri
Thu Oct 27, 2022 3:07 pm
Forum: NEURON + Python
Topic: record calcium concentration only from pyramidal cells
Replies: 2
Views: 186

record calcium concentration only from pyramidal cells

Hello I have a mod file that computes depolarization induced suppression of inhibition (DSI) which relies on the depolarization of the postsynaptic cell. For that, I need to access the calcium concentration of the postsynaptic cell that would be elevated upon depolarization. If I call"cai"...
by alexandrapierri
Wed Aug 10, 2022 10:37 pm
Forum: NEURON + Python
Topic: POINTER is not thread safe
Replies: 6
Views: 1006

Re: POINTER is not thread safe

Dear Ted I've attempted to correct the code according to your remarks. Here are some answers: The SOLVE statement refers to a non-existent equation block. This is a fatal problem. I now use cnexp which from what I have seen in numerous examples aside from differential equations is also used to solve...