Stochastic 3D model of neonatal rat spinal motoneuron (Ostroumov 2007)
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mso-level-number-position:left; text-indent:-18.0pt;} @list l0:level5 {mso-level-tab-stop:180.0pt; mso-level-number-position:left; text-indent:-18.0pt;} @list l0:level6 {mso-level-tab-stop:216.0pt; mso-level-number-position:left; text-indent:-18.0pt;} @list l0:level7 {mso-level-tab-stop:252.0pt; mso-level-number-position:left; text-indent:-18.0pt;} @list l0:level8 {mso-level-tab-stop:288.0pt; mso-level-number-position:left; text-indent:-18.0pt;} @list l0:level9 {mso-level-tab-stop:324.0pt; mso-level-number-position:left; text-indent:-18.0pt;} ol {margin-bottom:0cm;} ul {margin-bottom:0cm;} --> </style> <!--[if gte mso 10]> <style> /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman"; mso-ansi-language:#0400; mso-fareast-language:#0400; mso-bidi-language:#0400;} </style> <![endif]--><!--[if gte mso 9]><xml> <o:shapedefaults v:ext="edit" spidmax="3074"/> </xml><![endif]--><!--[if gte mso 9]><xml> <o:shapelayout v:ext="edit"> <o:idmap v:ext="edit" data="1"/> </o:shapelayout></xml><![endif]--> </head> <body lang=EN-US link=blue vlink=purple style='tab-interval:36.0pt'> <div class=Section1> <h1 align=center style='text-align:center'>Motoneuron-Morphology</h1> <p class=MsoNormal style='text-align:justify;line-height:150%'><o:p> </o:p></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'>Motoneuron-Morphology is a MATLAB based application, which simulates morphology of spinal motoneurons of the neonatal rat in the three dimensional space on the basis of experimental observations. Passive electrical properties and densities of three main voltage-activated (sodium and two potassium) channels can be selected for entire motoneuron or its sections. Subsequent application of the NEURON code for simulating the electrical properties of the modeled motoneuron is possible.<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><o:p> </o:p></p> <h2>Technical notes</h2> <p class=MsoNormal><o:p> </o:p></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'>Since NeuroMorphology was written as a MATLAB graphical user interface (GUI), it can only be run with MATLAB 6.5 (or later). MATLAB documentation and license information can be found on the <a href="http://www.mathworks.com/products/matlab/">MATLAB home page</a>. NEURON version 5.7.71 was freely downloaded from <a href="http://www.neuron.yale.edu/neuron/">NEURON home page</a> at <st1:place w:st="on"><st1:PlaceName w:st="on">Yale</st1:PlaceName> <st1:PlaceType w:st="on">University</st1:PlaceType></st1:place> and used for electrical simulation of modeled motoneuron. NEURON documentation if necessary can be found at the same site.<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><o:p> </o:p></p> <h2>Downloading and running of NeuroMorphology</h2> <p class=MsoNormal><o:p> </o:p></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'>NeuroMorphology can be downloaded from this site as a <i>NeuroMorph.zip</i> archive containing the following eight MATLAB files and one folder (<i>neuron</i>) with additional six NEURON files:<o:p></o:p></span></p> <p class=MsoNormal style='margin-left:36.0pt;text-align:justify;text-indent: -18.0pt;line-height:150%;mso-list:l0 level1 lfo2;tab-stops:list 36.0pt'><![if !supportLists]><span style='font-size:14.0pt;line-height:150%;font-family:Symbol;mso-fareast-font-family: Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><i><span style='font-size:14.0pt;line-height: 150%'>axon.m</span></i><span style='font-size:14.0pt;line-height:150%'> � M-file contains <i>axon</i> function which builds axon hillock, initial segment and axon proper with default or user defined lengths and diameters;<i><o:p></o:p></i></span></p> <p class=MsoNormal style='margin-left:36.0pt;text-align:justify;text-indent: -18.0pt;line-height:150%;mso-list:l0 level1 lfo2;tab-stops:list 36.0pt'><![if !supportLists]><span style='font-size:14.0pt;line-height:150%;font-family:Symbol;mso-fareast-font-family: Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><i><span style='font-size:14.0pt;line-height: 150%'>dendrites.m</span></i><span style='font-size:14.0pt;line-height:150%'> � M-file contains <i>dendrites</i> function which simulates the dendritic tree of the motoneuron on the basis of stochastic variations of dendritic tree dimensions in the default or user defined boundaries;<i><o:p></o:p></i></span></p> <p class=MsoNormal style='margin-left:36.0pt;text-align:justify;text-indent: -18.0pt;line-height:150%;mso-list:l0 level1 lfo2;tab-stops:list 36.0pt'><![if !supportLists]><span style='font-size:14.0pt;line-height:150%;font-family:Symbol;mso-fareast-font-family: Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><i><span style='font-size:14.0pt;line-height: 150%'>dendrogram</span></i><span style='font-size:14.0pt;line-height:150%'>.<i>m</i> � M-file contains <i>dendrogram</i> function which calculates relative complexity and builds a dendrogram of modeled motoneuron;<i><o:p></o:p></i></span></p> <p class=MsoNormal style='margin-left:36.0pt;text-align:justify;text-indent: -18.0pt;line-height:150%;mso-list:l0 level1 lfo2;tab-stops:list 36.0pt'><![if !supportLists]><span style='font-size:14.0pt;line-height:150%;font-family:Symbol;mso-fareast-font-family: Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><i><span style='font-size:14.0pt;line-height: 150%'>NeuroMorphology.fig</span></i><span style='font-size:14.0pt;line-height: 150%'> � file contains a complete description of the NeuroMorphology GUI figure layout and its components. This GUI should be selected from the MATLAB Open Existing GUI dialog (enter GUIDE at the MATLAB prompt);<i><o:p></o:p></i></span></p> <p class=MsoNormal style='margin-left:36.0pt;text-align:justify;text-indent: -18.0pt;line-height:150%;mso-list:l0 level1 lfo2;tab-stops:list 36.0pt'><![if !supportLists]><span style='font-size:14.0pt;line-height:150%;font-family:Symbol;mso-fareast-font-family: Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><i><span style='font-size:14.0pt;line-height: 150%'>NeuroMorphology</span></i><span style='font-size:14.0pt;line-height:150%'>.<i>m</i> � M-file that contains the code that controls the NeuroMorphology GUI, including the callbacks for its components;<i><o:p></o:p></i></span></p> <p class=MsoNormal style='margin-left:36.0pt;text-align:justify;text-indent: -18.0pt;line-height:150%;mso-list:l0 level1 lfo2;tab-stops:list 36.0pt'><![if !supportLists]><span style='font-size:14.0pt;line-height:150%;font-family:Symbol;mso-fareast-font-family: Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><i><span style='font-size:14.0pt;line-height: 150%'>soma.m</span></i><span style='font-size:14.0pt;line-height:150%'> � M-file is responsible for creating the soma as a prolate spheroid with the default or user defined dimensions;<i><o:p></o:p></i></span></p> <p class=MsoNormal style='margin-left:36.0pt;text-align:justify;text-indent: -18.0pt;line-height:150%;mso-list:l0 level1 lfo2;tab-stops:list 36.0pt'><![if !supportLists]><span style='font-size:14.0pt;line-height:150%;font-family:Symbol;mso-fareast-font-family: Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><i><span style='font-size:14.0pt;line-height: 150%'>To_NEURON.fig</span></i><span style='font-size:14.0pt;line-height:150%'> � file contains a complete description of the To_NEURON GUI figure layout and its components. To_NEURON GIU is loaded from the NeuroMorphology interface after clicking on the NEURON button;<i><o:p></o:p></i></span></p> <p class=MsoNormal style='margin-left:36.0pt;text-align:justify;text-indent: -18.0pt;line-height:150%;mso-list:l0 level1 lfo2;tab-stops:list 36.0pt'><![if !supportLists]><span style='font-size:14.0pt;line-height:150%;font-family:Symbol;mso-fareast-font-family: Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><i><span style='font-size:14.0pt;line-height: 150%'>To_NEURON</span></i><span style='font-size:14.0pt;line-height:150%'>.<i>m </i>� M-file that contains the code that controls the To_NEURON GUI and its callbacks;<i><o:p></o:p></i></span></p> <p class=MsoNormal style='margin-left:36.0pt;text-align:justify;text-indent: -18.0pt;line-height:150%;mso-list:l0 level1 lfo2;tab-stops:list 36.0pt'><![if !supportLists]><span style='font-size:14.0pt;line-height:150%;font-family:Symbol;mso-fareast-font-family: Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><i><span style='font-size:14.0pt;line-height: 150%'>neuron/electrical.hoc</span></i><span style='font-size:14.0pt;line-height: 150%'> � file contains set of commands which should be loaded to NEURON to define electrical properties of modeled motoneuron;<i><o:p></o:p></i></span></p> <p class=MsoNormal style='margin-left:36.0pt;text-align:justify;text-indent: -18.0pt;line-height:150%;mso-list:l0 level1 lfo2;tab-stops:list 36.0pt'><![if !supportLists]><span style='font-size:14.0pt;line-height:150%;font-family:Symbol;mso-fareast-font-family: Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><i><span style='font-size:14.0pt;line-height: 150%'>neuron/IKaSM.mod</span></i><span style='font-size:14.0pt;line-height: 150%'> � file contains description of the potassium fast (<i>K<sub>A</sub></i>)<i> </i>current specific for spinal motoneurons which was used for our simulation (see Safronov <i>et al.,</i> 2000);<i><o:p></o:p></i></span></p> <p class=MsoNormal style='margin-left:36.0pt;text-align:justify;text-indent: -18.0pt;line-height:150%;mso-list:l0 level1 lfo2;tab-stops:list 36.0pt'><![if !supportLists]><span style='font-size:14.0pt;line-height:150%;font-family:Symbol;mso-fareast-font-family: Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><i><span style='font-size:14.0pt;line-height: 150%'>neuron/IKdrSM.mod</span></i><span style='font-size:14.0pt;line-height: 150%'> � file contains description of the potassium delayed rectifier (<i>K<sub>DR</sub></i>)<i> </i>current expressed in the spinal motoneurons which was used for our simulation (see Safronov <i>et al.,</i> 2000);<i><o:p></o:p></i></span></p> <p class=MsoNormal style='margin-left:36.0pt;text-align:justify;text-indent: -18.0pt;line-height:150%;mso-list:l0 level1 lfo2;tab-stops:list 36.0pt'><![if !supportLists]><span style='font-size:14.0pt;line-height:150%;font-family:Symbol;mso-fareast-font-family: Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><i><span style='font-size:14.0pt;line-height: 150%'>neuron/INaSM.mod</span></i><span style='font-size:14.0pt;line-height: 150%'> � file contains description of the sodium current specific for spinal motoneurons which was used for our simulation (see Safronov <i>et al.,</i> 2000);<i><o:p></o:p></i></span></p> <p class=MsoNormal style='margin-left:36.0pt;text-align:justify;text-indent: -18.0pt;line-height:150%;mso-list:l0 level1 lfo2;tab-stops:list 36.0pt'><![if !supportLists]><span style='font-size:14.0pt;line-height:150%;font-family:Symbol;mso-fareast-font-family: Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><i><span style='font-size:14.0pt;line-height: 150%'>neuron/motoneuron</span></i><span style='font-size:14.0pt;line-height: 150%'>.<i>hoc</i> � file contains set of commands which produce loading of the modeled motoneuron�s morphology into the NEURON;<i><o:p></o:p></i></span></p> <p class=MsoNormal style='margin-left:36.0pt;text-align:justify;text-indent: -18.0pt;line-height:150%;mso-list:l0 level1 lfo2;tab-stops:list 36.0pt'><![if !supportLists]><span style='font-size:14.0pt;line-height:150%;font-family:Symbol;mso-fareast-font-family: Symbol;mso-bidi-font-family:Symbol;mso-bidi-font-style:italic'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><i><span style='font-size:14.0pt;line-height: 150%'>neuron/nrnmech</span></i><span style='font-size:14.0pt;line-height:150%'>.<i>dll</i> � file contains compiled mechanisms (<i>IKaSM, IKdrSM and INaSM</i>) and should be loaded to NEURON for simulation of voltage-dependent currents.<i><o:p></o:p></i></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><o:p> </o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'>Unpack <i>NeuroMorph.zip</i> archive into a MATLAB current directory and open <i>NeuroMorphology.fig</i> as an Existing GUI using MATLAB standard procedure. Briefly, to open NeuroMorphology enter GUIDE at the MATLAB prompt, go to the GUIDE Open Existing GUI dialog and open <i>NeuroMorphology.fig</i>. After opening the GUI, you can run it by selecting <b>Run</b> from the <b>Tools</b> menu or clicking the <b>Run</b> button on the GUIDE toolbar. If the directory where you unpack the <i>NeuroMorph.zip</i> is not on the MATLAB path change the current working directory to the directory containing <i>NeuroMorphology.fig</i> or add that directory to the MATLAB path.</span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><o:p> </o:p></p> <h2>Using NeuroMorphology (an example)</h2> <p class=MsoNormal><o:p> </o:p></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'>After running the NeuroMorphology its graphical user interface will appear.<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'>Picture below briefly introduces main parts of the interface</span>.</p> <p class=MsoNormal style='text-align:justify;line-height:150%'><!--[if gte vml 1]><v:shapetype id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t" path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f"> <v:stroke joinstyle="miter"/> <v:formulas> <v:f eqn="if lineDrawn pixelLineWidth 0"/> <v:f eqn="sum @0 1 0"/> <v:f eqn="sum 0 0 @1"/> <v:f eqn="prod @2 1 2"/> <v:f eqn="prod @3 21600 pixelWidth"/> <v:f eqn="prod @3 21600 pixelHeight"/> <v:f eqn="sum @0 0 1"/> <v:f eqn="prod @6 1 2"/> <v:f eqn="prod @7 21600 pixelWidth"/> <v:f eqn="sum @8 21600 0"/> <v:f eqn="prod @7 21600 pixelHeight"/> <v:f eqn="sum @10 21600 0"/> </v:formulas> <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/> <o:lock v:ext="edit" aspectratio="t"/> </v:shapetype><v:shape id="_x0000_i1025" type="#_x0000_t75" style='width:10in; height:479.25pt'> <v:imagedata src="readme_files/image001.gif" o:title="ModelMain"/> </v:shape><![endif]--><![if !vml]><img border=0 width=960 height=639 src="readme_files/image002.jpg" v:shapes="_x0000_i1025"><![endif]></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><o:p> </o:p></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'>Let�s leave all the parameters as they are and just click on the <b style='mso-bidi-font-weight:normal'>Start</b> button. Relative complexity graph and dendrogram would appear in the main window. Plus additional window with 3D neuron representation should become visible. MATLAB provides a set of useful tools to rotate, zoom in/out and save the 3D image.<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><o:p> </o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><!--[if gte vml 1]><v:shape id="_x0000_i1026" type="#_x0000_t75" style='width:730.5pt;height:424.5pt'> <v:imagedata src="readme_files/image003.gif" o:title="ModelAfterStart"/> </v:shape><![endif]--><![if !vml]><img border=0 width=974 height=566 src="readme_files/image003.gif" v:shapes="_x0000_i1026"><![endif]><o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><o:p> </o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'>To get numerical values describing simulated neuron click the <b style='mso-bidi-font-weight:normal'>Report</b> button on the main panel. The <i style='mso-bidi-font-style:normal'>Report</i> file will appear in the MATLAB current directory. Sometimes it can be useful to save current setting (dimensions) in the separate file to compare different results or analyze data. To do so, click on the <b style='mso-bidi-font-weight: normal'>Setting</b> button (after clicking <i style='mso-bidi-font-style:normal'>Settings</i> file will appear in the MATLAB current directory). For abbreviations and terms see <a href="Glossary.html" target=Frame1>Glossary</a>.<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><o:p> </o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><!--[if gte vml 1]><v:shape id="_x0000_i1027" type="#_x0000_t75" style='width:654.75pt;height:307.5pt'> <v:imagedata src="readme_files/image004.gif" o:title="Report and Settings"/> </v:shape><![endif]--><![if !vml]><img border=0 width=873 height=410 src="readme_files/image005.jpg" v:shapes="_x0000_i1027"><![endif]><o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'>If we are satisfied with the simulated neuron in terms of its morphology, let�s try to introduce distributed voltage-dependent currents. Click on the <b style='mso-bidi-font-weight:normal'>NEURON</b> button on the main window. To_NEURON dialog will appear. The following picture describes this dialog window.<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><o:p> </o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><!--[if gte vml 1]><v:shape id="_x0000_i1028" type="#_x0000_t75" style='width:630pt;height:423.75pt'> <v:imagedata src="readme_files/image006.gif" o:title="To_Neuron_Full"/> </v:shape><![endif]--><![if !vml]><img border=0 width=840 height=565 src="readme_files/image007.jpg" v:shapes="_x0000_i1028"><![endif]><o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><o:p> </o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'>At this point we would like to change <i style='mso-bidi-font-style:normal'>Na<sup>+</sup>, Ka </i>and <i style='mso-bidi-font-style:normal'>Kdr</i> conductances to certain values. After doing this To_NEURON dialog window should look like the following:<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><o:p> </o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><!--[if gte vml 1]><v:shape id="_x0000_i1029" type="#_x0000_t75" style='width:574.5pt;height:264.75pt'> <v:imagedata src="readme_files/image008.jpg" o:title="To_Neuron_Filled"/> </v:shape><![endif]--><![if !vml]><img border=0 width=766 height=353 src="readme_files/image008.jpg" v:shapes="_x0000_i1029"><![endif]><o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><o:p> </o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'>Click on the <b style='mso-bidi-font-weight: normal'>Generate NEURON code</b> button to prepare data for electrical simulation. Now all the data are transformed to the code for further use with the NEURON simulator and saved in the MATLAB current directory�s folder <i style='mso-bidi-font-style:normal'>neuron</i> (if you unpack the NeuroMorphology archive rather than the MATLAB current directory, it is useful to copy all six NEURON files to the folder <i style='mso-bidi-font-style:normal'>neuron</i> now).<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><o:p> </o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><!--[if gte vml 1]><v:shape id="_x0000_i1030" type="#_x0000_t75" style='width:407.25pt;height:339.75pt'> <v:imagedata src="readme_files/image009.gif" o:title="neuronfolder"/> </v:shape><![endif]--><![if !vml]><img border=0 width=543 height=453 src="readme_files/image009.gif" v:shapes="_x0000_i1030"><![endif]><o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><o:p> </o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'>Files with <i style='mso-bidi-font-style: normal'>.dat</i> extension are created by NeuroMorphology, their names indicate their content.<o:p></o:p></span></p> <h2>NeuroMorphology and NEURON<span style='font-style:normal;mso-bidi-font-style: italic'><o:p></o:p></span></h2> <p class=MsoNormal style='line-height:150%'><span style='font-size:14.0pt; line-height:150%'><o:p> </o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'>First of all, change the NEURON working directory to the <i style='mso-bidi-font-style:normal'>neuron</i> folder in the MATLAB working directory (it may be useful to copy simulation results to some another directory if you are going to create a network or something like this). If NEURON was installed properly, it should detect <i style='mso-bidi-font-style: normal'>nrnmech.dll</i> file in this directory and load membrane �mechanism� from it (<i style='mso-bidi-font-style:normal'>INaSM, IKaSM</i> and <i style='mso-bidi-font-style:normal'>IKdrSM</i>).<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'>Commands translating neuron morphology into NEURON are located in the <i style='mso-bidi-font-style:normal'>motoneuron.hoc</i> file. Once this file has been loaded to NEURON, it automatically reads data from all generated files except <i style='mso-bidi-font-style:normal'>.dat</i> files whose name starts with �tree� (<i style='mso-bidi-font-style:normal'>tree1.dat</i> for example). NEURON will ask you to choose these files one by one as it shown here.<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><o:p> </o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><i style='mso-bidi-font-style:normal'><span style='font-size:14.0pt;line-height: 150%'><!--[if gte vml 1]><v:shape id="_x0000_i1031" type="#_x0000_t75" style='width:161.25pt; height:204.75pt'> <v:imagedata src="readme_files/image010.gif" o:title="neuronstep3"/> </v:shape><![endif]--><![if !vml]><img border=0 width=215 height=273 src="readme_files/image010.gif" v:shapes="_x0000_i1031"><![endif]></span></i><span style='font-size:14.0pt;line-height:150%'><o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><o:p> </o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'>After you finish loading morphology, the next step is to load electrical properties of the simulated neuron. For this use <i style='mso-bidi-font-style:normal'>electrical.hoc</i>. Now everything is ready for simulation. By default, we introduced �single pulse current clamp point process�</span> <span style='font-size:14.0pt;line-height: 150%'>into the center of the soma (IClamp[0] at soma 0.5). Open the Voltage axis graph and the RunControl panel, then press <b style='mso-bidi-font-weight: normal'>Init & Run<i style='mso-bidi-font-style:normal'> </i></b>button to see the voltage response of the simulated neuron to the current step of 0.5 nA amplitude applied to the center of the soma. Results and NEURONS�s panels are shown below. We just opened �Distributed Mechanism viewer/Shape Name/soma� to insure that we have correctly loaded the simulated neuron. The dimensions and electrical properties of the soma are the same as in the Soma report and To_Neuron dialog (see above).<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%'><span style='font-size:14.0pt;line-height:150%'><o:p> </o:p></span></p> <p class=MsoNormal style='line-height:150%'><span style='font-size:14.0pt; line-height:150%'><!--[if gte vml 1]><v:shape id="_x0000_i1032" type="#_x0000_t75" style='width:739.5pt;height:718.5pt'> <v:imagedata src="readme_files/image011.gif" o:title="NeuronFull1"/> </v:shape><![endif]--><![if !vml]><img border=0 width=986 height=958 src="readme_files/image011.gif" v:shapes="_x0000_i1032"><![endif]><o:p></o:p></span></p> </div> </body> </html>
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Stochastic 3D model of neonatal rat spinal motoneuron (Ostroumov 2007)
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