Search found 69 matches

by alexandrapierri
Fri Jul 21, 2023 4:19 pm
Forum: Anatomically detailed models
Topic: Setting RMP according to experimental measurements.
Replies: 5
Views: 23538

Re: Setting RMP according to experimental measurements.

yes, many mechanisms do USEION and then WRITE concentrations of ions such as those describing calcium concentrations, Na and potassium channels.
by alexandrapierri
Fri Jul 21, 2023 3:36 pm
Forum: Anatomically detailed models
Topic: Setting RMP according to experimental measurements.
Replies: 5
Views: 23538

Re: Setting RMP according to experimental measurements.

I use this model by Aberra et al 2018. https://senselab.med.yale.edu/ModelDB/ShowModel?model=241165 These are L23 cortical pyramidal cells that are driven by synaptic events from other cortical layers. I have replaced the morphologies with morphogies of L23 pyramidal cells given to me by my experime...
by alexandrapierri
Thu Jul 20, 2023 7:48 pm
Forum: Anatomically detailed models
Topic: Setting RMP according to experimental measurements.
Replies: 5
Views: 23538

Setting RMP according to experimental measurements.

Hello NEURON community I set the RMP of my model cell to a certain value, i.e at -69mV but as soon as the simulation starts the RMP becomes hyperpolized. I realize this can be an effect of ion channels combined with morpholgical aspects causing the RMP to drop at a lower value than what I set it at ...
by alexandrapierri
Wed May 10, 2023 11:49 pm
Forum: Anatomically detailed models
Topic: All or none action potentials?
Replies: 1
Views: 15491

All or none action potentials?

Hello

Are the action potentials modeled using mutlicompartmental modeling in NEURON all or none?
If yes what is the minimum amplitude of an action potential (30, 40mV less than that)? Should events overshooting 0mV be considered as APs or as subthreshold EPSPs?

thank you,
A
by alexandrapierri
Mon Mar 20, 2023 10:33 pm
Forum: Anatomically detailed models
Topic: Segmentation violation error in swc
Replies: 4
Views: 16031

Re: Segmentation violation error in swc

I see, understood.Thank you!
by alexandrapierri
Mon Mar 20, 2023 5:13 pm
Forum: Anatomically detailed models
Topic: Segmentation violation error in swc
Replies: 4
Views: 16031

Re: Segmentation violation error in swc

thank you very much for your response Ted Regarding point 2. indeed I have noticed this myself and had decided to artifially add radius. Based on the data at my disposal I can estimate average radius per section. I have 4 sections, so four average radius values. That is not an ideal solution but my ...
by alexandrapierri
Fri Mar 17, 2023 3:15 pm
Forum: Anatomically detailed models
Topic: Segmentation violation error in swc
Replies: 4
Views: 16031

Segmentation violation error in swc

Hello I load this morphology with "new Import3d_SWC_read()" and when I plot the voltage, I get a segmentation violation error. I have used similar morphologies and others worked well. Unsure what I should be looking for that would be causing this error. Is it a discontinuity in the SWC poi...
by alexandrapierri
Fri Mar 10, 2023 7:48 pm
Forum: The GUI
Topic: recording HCN channels using GUI
Replies: 7
Views: 13967

Re: recording HCN channels using GUI

thank you Ted! Repetetion of fundamental concepts is very fruitful. It is very true that in person interactions are many times better, however through this forum you've been nothing but a great teacher and a mentor to all of us. I would like to illustrate my issue in this context with a specific exa...
by alexandrapierri
Wed Mar 08, 2023 6:35 pm
Forum: The GUI
Topic: recording HCN channels using GUI
Replies: 7
Views: 13967

Re: recording HCN channels using GUI

that sounds very good, thank you. I will post here my solution. One clarification that always confuses me. I dont want to "add" a distributed mechanism to the model. The model already has distributed mechanisms added to it an I want to write a voltage clamp experiment to record them (speci...
by alexandrapierri
Wed Mar 08, 2023 5:23 pm
Forum: The GUI
Topic: recording HCN channels using GUI
Replies: 7
Views: 13967

Re: recording HCN channels using GUI

thank you Ted I am doing a voltage clamp on my pyramidal cell to record Ih under different holding potentials. Following your steps I write: pyr1 = h.cADpyr229_L23_PC_c2e79db05a # name of the cell template defined next to begintemplate in the model hoc file. pyr1_v_vec = h.Vector() pyr1_i_vec = h.Ve...
by alexandrapierri
Tue Mar 07, 2023 3:36 pm
Forum: The GUI
Topic: recording HCN channels using GUI
Replies: 7
Views: 13967

recording HCN channels using GUI

Hello I want to record the HCN currents per some surface area in my multicompartment model using GUI. I have searched through the following links but haven't found relevant insructions yet. https://nrn.readthedocs.io/en/latest/search.html?q=GUI+record+Ih+&check_keywords=yes&area=default Than...
by alexandrapierri
Fri Feb 24, 2023 9:17 pm
Forum: Anatomically detailed models
Topic: cells don't fire without axon
Replies: 1
Views: 10443

cells don't fire without axon

hello I am using a L23 pyramidal neuron from the HBP cortical microcircuit, Aberra et al 2018 https://senselab.med.yale.edu/ModelDB/S ... del=241165. I replace the morphology of a L23 cortical cell with my own morphology, but I preserve mechnanisms and synapse distribution from the HBP. If I use sol...
by alexandrapierri
Fri Feb 24, 2023 9:08 pm
Forum: Anatomically detailed models
Topic: EOF in fscan
Replies: 2
Views: 10408

Re: EOF in fscan

yes the file being scanned was corrupted. I fixed it, thank you!
by alexandrapierri
Mon Feb 20, 2023 5:54 pm
Forum: Anatomically detailed models
Topic: EOF in fscan
Replies: 2
Views: 10408

EOF in fscan

hello I am using a L23 pyramidal neuron from the HBP cortical microcircuit, Aberra et al 2018 https://senselab.med.yale.edu/ModelDB/ShowModel?model=241165 . I replace the morphology of a L23 cortical cell with my own morphology, but I preserve mechnanisms and synapse distribution from the HBP. If th...
by alexandrapierri
Wed Jan 04, 2023 7:32 pm
Forum: Anatomically detailed models
Topic: SWC file content
Replies: 6
Views: 13106

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