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In this version of LFPsim, the ion channel distribution density and size of the individual compaertments was considered in the LFP calculation.
This is the README for the model associated with the paper:
Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar
S. Computational Modeling of Single Neuron Extracellular Electric
Potentials and Network Local Field Potentials using LFPsim,
Front. Comp. Neurosc., June 13, 2016, 10.3389/fncom.2016.00065
available at
http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/abstract
LFPsim - Simulation scripts to compute Local Field Potentials (LFP)
from cable compartmental models of neurons and networks implemented in
NEURON simulation environment.
LFPsim works reliably on biophysically detailed multi-compartmental
neurons with ion channels in some or all compartments.
Associated Paper:
Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar
S. Computational Modeling of Single Neuron Extracellular Electric
Potentials and Network Local Field Potentials using LFPsim,
Front. Comp. Neurosc., June 13, 2016, 10.3389/fncom.2016.00065
available at
http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/abstract
Edited with inputs on a bug related to area. Thanks to Lucas Koelman for the corrections (https://github.com/lkoelman). Last updated 25-June-2018
Developed by : Harilal Parasuram & Shyam Diwakar
Computational Neuroscience & Neurophysiology Lab, School of Biotechnology, Amrita University, India.
Email: harilalp@am.amrita.edu; shyam@amrita.edu
www.amrita.edu/compneuro */
How to run LFPsim
=================
1. Copy all LFPsim files and the directory into your NEURON model
directory downloaded from ModelDB. Copy lfp.mod and mea.mod from
LFPsim to the mechanism directory of the NEURON model.
2. Compile the model; if you had already compiled the model without
LFPsim, include the LFPsim mod files and re-compile using "nrnivmodl"
or "mknrndll".
3. Load your neuron or network model in NEURON.
4. On the terminal type: xopen("extracellular_electrode.hoc") to
initiate LFPsim GUI interface.
5. Set the electrode properties in the GUI.
6. Run the simulation to reconstruct LFP.
A detailed step-by-step procedure is also listed in the
How-To-LFPsim.pdf document.

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Simulation scripts to compute Local Field Potentials (LFP) of cable compartmental models implemented with NEURON

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In this version of LFPsim, the ion channel distribution density and size of the individual compaertments was considered in the LFP calculation.
This is the README for the model associated with the paper:
Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar
S. Computational Modeling of Single Neuron Extracellular Electric
Potentials and Network Local Field Potentials using LFPsim,
Front. Comp. Neurosc., June 13, 2016, 10.3389/fncom.2016.00065
available at
http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/abstract
LFPsim - Simulation scripts to compute Local Field Potentials (LFP)
from cable compartmental models of neurons and networks implemented in
NEURON simulation environment.
LFPsim works reliably on biophysically detailed multi-compartmental
neurons with ion channels in some or all compartments.
Associated Paper:
Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar
S. Computational Modeling of Single Neuron Extracellular Electric
Potentials and Network Local Field Potentials using LFPsim,
Front. Comp. Neurosc., June 13, 2016, 10.3389/fncom.2016.00065
available at
http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/abstract
Edited with inputs on a bug related to area. Thanks to Lucas Koelman for the corrections (https://github.com/lkoelman). Last updated 25-June-2018
Developed by : Harilal Parasuram & Shyam Diwakar
Computational Neuroscience & Neurophysiology Lab, School of Biotechnology, Amrita University, India.
Email: harilalp@am.amrita.edu; shyam@amrita.edu
www.amrita.edu/compneuro */
How to run LFPsim
=================
1. Copy all LFPsim files and the directory into your NEURON model
directory downloaded from ModelDB. Copy lfp.mod and mea.mod from
LFPsim to the mechanism directory of the NEURON model.
2. Compile the model; if you had already compiled the model without
LFPsim, include the LFPsim mod files and re-compile using "nrnivmodl"
or "mknrndll".
3. Load your neuron or network model in NEURON.
4. On the terminal type: xopen("extracellular_electrode.hoc") to
initiate LFPsim GUI interface.
5. Set the electrode properties in the GUI.
6. Run the simulation to reconstruct LFP.
A detailed step-by-step procedure is also listed in the
How-To-LFPsim.pdf document.

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Simulation scripts to compute Local Field Potentials (LFP) of cable compartmental models implemented with NEURON
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In this version of LFPsim, the ion channel distribution density and size of the individual compaertments was considered in the LFP calculation.
This is the README for the model associated with the paper:
Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar
S. Computational Modeling of Single Neuron Extracellular Electric
Potentials and Network Local Field Potentials using LFPsim,
Front. Comp. Neurosc., June 13, 2016, 10.3389/fncom.2016.00065
available at
http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/abstract
LFPsim - Simulation scripts to compute Local Field Potentials (LFP)
from cable compartmental models of neurons and networks implemented in
NEURON simulation environment.
LFPsim works reliably on biophysically detailed multi-compartmental
neurons with ion channels in some or all compartments.
Associated Paper:
Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar
S. Computational Modeling of Single Neuron Extracellular Electric
Potentials and Network Local Field Potentials using LFPsim,
Front. Comp. Neurosc., June 13, 2016, 10.3389/fncom.2016.00065
available at
http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/abstract
Edited with inputs on a bug related to area. Thanks to Lucas Koelman for the corrections (https://github.com/lkoelman). Last updated 25-June-2018
Developed by : Harilal Parasuram & Shyam Diwakar
Computational Neuroscience & Neurophysiology Lab, School of Biotechnology, Amrita University, India.
Email: harilalp@am.amrita.edu; shyam@amrita.edu
www.amrita.edu/compneuro */
How to run LFPsim
=================
1. Copy all LFPsim files and the directory into your NEURON model
directory downloaded from ModelDB. Copy lfp.mod and mea.mod from
LFPsim to the mechanism directory of the NEURON model.
2. Compile the model; if you had already compiled the model without
LFPsim, include the LFPsim mod files and re-compile using "nrnivmodl"
or "mknrndll".
3. Load your neuron or network model in NEURON.
4. On the terminal type: xopen("extracellular_electrode.hoc") to
initiate LFPsim GUI interface.
5. Set the electrode properties in the GUI.
6. Run the simulation to reconstruct LFP.
A detailed step-by-step procedure is also listed in the
How-To-LFPsim.pdf document.

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Simulation scripts to compute Local Field Potentials (LFP) of cable compartmental models implemented with NEURON
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In this version of LFPsim, the ion channel distribution density and size of the individual compaertments was considered in the LFP calculation.
This is the README for the model associated with the paper:
Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar
S. Computational Modeling of Single Neuron Extracellular Electric
Potentials and Network Local Field Potentials using LFPsim,
Front. Comp. Neurosc., June 13, 2016, 10.3389/fncom.2016.00065
available at
http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/abstract
LFPsim - Simulation scripts to compute Local Field Potentials (LFP)
from cable compartmental models of neurons and networks implemented in
NEURON simulation environment.
LFPsim works reliably on biophysically detailed multi-compartmental
neurons with ion channels in some or all compartments.
Associated Paper:
Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar
S. Computational Modeling of Single Neuron Extracellular Electric
Potentials and Network Local Field Potentials using LFPsim,
Front. Comp. Neurosc., June 13, 2016, 10.3389/fncom.2016.00065
available at
http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/abstract
Edited with inputs on a bug related to area. Thanks to Lucas Koelman for the corrections (https://github.com/lkoelman). Last updated 25-June-2018
Developed by : Harilal Parasuram & Shyam Diwakar
Computational Neuroscience & Neurophysiology Lab, School of Biotechnology, Amrita University, India.
Email: harilalp@am.amrita.edu; shyam@amrita.edu
www.amrita.edu/compneuro */
How to run LFPsim
=================
1. Copy all LFPsim files and the directory into your NEURON model
directory downloaded from ModelDB. Copy lfp.mod and mea.mod from
LFPsim to the mechanism directory of the NEURON model.
2. Compile the model; if you had already compiled the model without
LFPsim, include the LFPsim mod files and re-compile using "nrnivmodl"
or "mknrndll".
3. Load your neuron or network model in NEURON.
4. On the terminal type: xopen("extracellular_electrode.hoc") to
initiate LFPsim GUI interface.
5. Set the electrode properties in the GUI.
6. Run the simulation to reconstruct LFP.
A detailed step-by-step procedure is also listed in the
How-To-LFPsim.pdf document.

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Simulation scripts to compute Local Field Potentials (LFP) of cable compartmental models implemented with NEURON
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
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In this version of LFPsim, the ion channel distribution density and size of the individual compaertments was considered in the LFP calculation.
This is the README for the model associated with the paper:
Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar
S. Computational Modeling of Single Neuron Extracellular Electric
Potentials and Network Local Field Potentials using LFPsim,
Front. Comp. Neurosc., June 13, 2016, 10.3389/fncom.2016.00065
available at
http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/abstract
LFPsim - Simulation scripts to compute Local Field Potentials (LFP)
from cable compartmental models of neurons and networks implemented in
NEURON simulation environment.
LFPsim works reliably on biophysically detailed multi-compartmental
neurons with ion channels in some or all compartments.
Associated Paper:
Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar
S. Computational Modeling of Single Neuron Extracellular Electric
Potentials and Network Local Field Potentials using LFPsim,
Front. Comp. Neurosc., June 13, 2016, 10.3389/fncom.2016.00065
available at
http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/abstract
Edited with inputs on a bug related to area. Thanks to Lucas Koelman for the corrections (https://github.com/lkoelman). Last updated 25-June-2018
Developed by : Harilal Parasuram & Shyam Diwakar
Computational Neuroscience & Neurophysiology Lab, School of Biotechnology, Amrita University, India.
Email: harilalp@am.amrita.edu; shyam@amrita.edu
www.amrita.edu/compneuro */
How to run LFPsim
=================
1. Copy all LFPsim files and the directory into your NEURON model
directory downloaded from ModelDB. Copy lfp.mod and mea.mod from
LFPsim to the mechanism directory of the NEURON model.
2. Compile the model; if you had already compiled the model without
LFPsim, include the LFPsim mod files and re-compile using "nrnivmodl"
or "mknrndll".
3. Load your neuron or network model in NEURON.
4. On the terminal type: xopen("extracellular_electrode.hoc") to
initiate LFPsim GUI interface.
5. Set the electrode properties in the GUI.
6. Run the simulation to reconstruct LFP.
A detailed step-by-step procedure is also listed in the
How-To-LFPsim.pdf document.

About
Simulation scripts to compute Local Field Potentials (LFP) of cable compartmental models implemented with NEURON
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In this version of LFPsim, the ion channel distribution density and size of the individual compaertments was considered in the LFP calculation.
This is the README for the model associated with the paper:
Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar
S. Computational Modeling of Single Neuron Extracellular Electric
Potentials and Network Local Field Potentials using LFPsim,
Front. Comp. Neurosc., June 13, 2016, 10.3389/fncom.2016.00065
available at
http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/abstract
LFPsim - Simulation scripts to compute Local Field Potentials (LFP)
from cable compartmental models of neurons and networks implemented in
NEURON simulation environment.
LFPsim works reliably on biophysically detailed multi-compartmental
neurons with ion channels in some or all compartments.
Associated Paper:
Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar
S. Computational Modeling of Single Neuron Extracellular Electric
Potentials and Network Local Field Potentials using LFPsim,
Front. Comp. Neurosc., June 13, 2016, 10.3389/fncom.2016.00065
available at
http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/abstract
Edited with inputs on a bug related to area. Thanks to Lucas Koelman for the corrections (https://github.com/lkoelman). Last updated 25-June-2018
Developed by : Harilal Parasuram & Shyam Diwakar
Computational Neuroscience & Neurophysiology Lab, School of Biotechnology, Amrita University, India.
Email: harilalp@am.amrita.edu; shyam@amrita.edu
www.amrita.edu/compneuro */
How to run LFPsim
=================
1. Copy all LFPsim files and the directory into your NEURON model
directory downloaded from ModelDB. Copy lfp.mod and mea.mod from
LFPsim to the mechanism directory of the NEURON model.
2. Compile the model; if you had already compiled the model without
LFPsim, include the LFPsim mod files and re-compile using "nrnivmodl"
or "mknrndll".
3. Load your neuron or network model in NEURON.
4. On the terminal type: xopen("extracellular_electrode.hoc") to
initiate LFPsim GUI interface.
5. Set the electrode properties in the GUI.
6. Run the simulation to reconstruct LFP.
A detailed step-by-step procedure is also listed in the
How-To-LFPsim.pdf document.

About
Simulation scripts to compute Local Field Potentials (LFP) of cable compartmental models implemented with NEURON
Resources
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Watchers
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Forks
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injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
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In this version of LFPsim, the ion channel distribution density and size of the individual compaertments was considered in the LFP calculation.
This is the README for the model associated with the paper:
Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar
S. Computational Modeling of Single Neuron Extracellular Electric
Potentials and Network Local Field Potentials using LFPsim,
Front. Comp. Neurosc., June 13, 2016, 10.3389/fncom.2016.00065
available at
http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/abstract
LFPsim - Simulation scripts to compute Local Field Potentials (LFP)
from cable compartmental models of neurons and networks implemented in
NEURON simulation environment.
LFPsim works reliably on biophysically detailed multi-compartmental
neurons with ion channels in some or all compartments.
Associated Paper:
Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar
S. Computational Modeling of Single Neuron Extracellular Electric
Potentials and Network Local Field Potentials using LFPsim,
Front. Comp. Neurosc., June 13, 2016, 10.3389/fncom.2016.00065
available at
http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/abstract
Edited with inputs on a bug related to area. Thanks to Lucas Koelman for the corrections (https://github.com/lkoelman). Last updated 25-June-2018
Developed by : Harilal Parasuram & Shyam Diwakar
Computational Neuroscience & Neurophysiology Lab, School of Biotechnology, Amrita University, India.
Email: harilalp@am.amrita.edu; shyam@amrita.edu
www.amrita.edu/compneuro */
How to run LFPsim
=================
1. Copy all LFPsim files and the directory into your NEURON model
directory downloaded from ModelDB. Copy lfp.mod and mea.mod from
LFPsim to the mechanism directory of the NEURON model.
2. Compile the model; if you had already compiled the model without
LFPsim, include the LFPsim mod files and re-compile using "nrnivmodl"
or "mknrndll".
3. Load your neuron or network model in NEURON.
4. On the terminal type: xopen("extracellular_electrode.hoc") to
initiate LFPsim GUI interface.
5. Set the electrode properties in the GUI.
6. Run the simulation to reconstruct LFP.
A detailed step-by-step procedure is also listed in the
How-To-LFPsim.pdf document.

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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
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In this version of LFPsim, the ion channel distribution density and size of the individual compaertments was considered in the LFP calculation.
This is the README for the model associated with the paper:
Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar
S. Computational Modeling of Single Neuron Extracellular Electric
Potentials and Network Local Field Potentials using LFPsim,
Front. Comp. Neurosc., June 13, 2016, 10.3389/fncom.2016.00065
available at
http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/abstract
LFPsim - Simulation scripts to compute Local Field Potentials (LFP)
from cable compartmental models of neurons and networks implemented in
NEURON simulation environment.
LFPsim works reliably on biophysically detailed multi-compartmental
neurons with ion channels in some or all compartments.
Associated Paper:
Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar
S. Computational Modeling of Single Neuron Extracellular Electric
Potentials and Network Local Field Potentials using LFPsim,
Front. Comp. Neurosc., June 13, 2016, 10.3389/fncom.2016.00065
available at
http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/abstract
Edited with inputs on a bug related to area. Thanks to Lucas Koelman for the corrections (https://github.com/lkoelman). Last updated 25-June-2018
Developed by : Harilal Parasuram & Shyam Diwakar
Computational Neuroscience & Neurophysiology Lab, School of Biotechnology, Amrita University, India.
Email: harilalp@am.amrita.edu; shyam@amrita.edu
www.amrita.edu/compneuro */
How to run LFPsim
=================
1. Copy all LFPsim files and the directory into your NEURON model
directory downloaded from ModelDB. Copy lfp.mod and mea.mod from
LFPsim to the mechanism directory of the NEURON model.
2. Compile the model; if you had already compiled the model without
LFPsim, include the LFPsim mod files and re-compile using "nrnivmodl"
or "mknrndll".
3. Load your neuron or network model in NEURON.
4. On the terminal type: xopen("extracellular_electrode.hoc") to
initiate LFPsim GUI interface.
5. Set the electrode properties in the GUI.
6. Run the simulation to reconstruct LFP.
A detailed step-by-step procedure is also listed in the
How-To-LFPsim.pdf document.

About
Simulation scripts to compute Local Field Potentials (LFP) of cable compartmental models implemented with NEURON
Resources
Readme
Activity
Stars
9 stars
Watchers
3 watching
Forks
6 forks
Report repository
Releases
Packages
Contributors
Languages