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| 2 | ·cc5357c7c7dcd595dae0cc6054c19514·4565964·python·optional·python3-bmtk-examples_0.0+git20210109.8572664+ds-1_all.deb | 2 | ·cc5357c7c7dcd595dae0cc6054c19514·4565964·python·optional·python3-bmtk-examples_0.0+git20210109.8572664+ds-1_all.deb |
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| 1157 | <div·class="section"·id="Units"> | 1157 | <div·class="section"·id="Units"> |
| 1158 | <h2>Units<a·class="headerlink"·href="#Units"·title="Permalink·to·this·headline">¶</a></h2> | 1158 | <h2>Units<a·class="headerlink"·href="#Units"·title="Permalink·to·this·headline">¶</a></h2> |
| 1159 | <div·class="section"·id="simple-ON/OFF-cells"> | 1159 | <div·class="section"·id="simple-ON/OFF-cells"> |
| 1160 | <h3>simple·ON/OFF·cells<a·class="headerlink"·href="#simple-ON/OFF-cells"·title="Permalink·to·this·headline">¶</a></h3> | 1160 | <h3>simple·ON/OFF·cells<a·class="headerlink"·href="#simple-ON/OFF-cells"·title="Permalink·to·this·headline">¶</a></h3> |
| 1161 | <p>These·are·cells·that·respond·by·either·increasing·or·decreasing·firing·rates·to·brightness·changes·in·their·receptive·fields.·They·are·also·the·basis·for·more·advanced·cell·types.·When·building·a·network·you·can·set·a·cell·or·set·of·cells·with·<code·class="docutils·literal·notranslate"><span·class="pre">model_template='lgnmodel:tON'</span></code>·or·<code·class="docutils·literal·notranslate"><span·class="pre">model_template='lgnmodel:tOFF'</span></code>·during·the·call·to·<code·class="docutils·literal·notranslate"><span·class="pre">add_nodes(...)</span></code>.·There·are·also·a·number·of·special·types | 1161 | <p>These·are·cells·that·respond·by·either·increasing·or·decreasing·firing·rates·to·brightness·changes·in·their·receptive·fields.·They·are·also·the·basis·for·more·advanced·cell·types.·When·building·a·network·you·can·set·a·cell·or·set·of·cells·with·<code·class="docutils·literal·notranslate"><span·class="pre">model_template='lgnmodel:tON'</span></code>·or·<code·class="docutils·literal·notranslate"><span·class="pre">model_template='lgnmodel:tOFF'</span></code>·during·the·call·to·<code·class="docutils·literal·notranslate"><span·class="pre">add_nodes(...)</span></code>.·There·are·also·a·number·of·special·types |
| 1162 | (<code·class="docutils·literal·notranslate"><span·class="pre">tON_TF8,</span>·<span·class="pre">sON_TF1,</span>·<span·class="pre">sON_TF2,</span>·<span·class="pre">sON_TF4,</span>·<span·class="pre">sON_TF8,</span>·<span·class="pre">sON_TF15,</span>·<span·class="pre">tOFF_TF1,</span>·<span·class="pre">tOFF_TF2,</span>·<span·class="pre">tOFF_TF4,</span>·<span·class="pre">tOFF_TF8,</span>·<span·class="pre">tOFF_TF15,</span>·<span·class="pre">sOFF_TF1,</span>·<span·class="pre">sOFF_TF2,</span>·<span·class="pre">sOFF_TF4,</span>·<span·class="pre">sOFF_TF8,</span>·<span·class="pre">sOFF_TF15</span></code>)·which·have·properties·that·have·been·pre-calculated·using·electrophysiological·recordings·from·the·mouse·LGN·(Durant·et.·al·2016,·Billeh·et.·al·2019).</p> | 1162 | (<code·class="docutils·literal·notranslate"><span·class="pre">tON_TF8,</span>·<span·class="pre">sON_TF1,</span>·<span·class="pre">sON_TF2,</span>·<span·class="pre">sON_TF4,</span>·<span·class="pre">sON_TF8,</span>·<span·class="pre">sON_TF15,</span>·<span·class="pre">tOFF_TF1,</span>·<span·class="pre">tOFF_TF2,</span>·<span·class="pre">tOFF_TF4,</span>·<span·class="pre">tOFF_TF8,</span>·<span·class="pre">tOFF_TF15,</span>·<span·class="pre">sOFF_TF1,</span>·<span·class="pre">sOFF_TF2,</span>·<span·class="pre">sOFF_TF4,</span>·<span·class="pre">sOFF_TF8,</span>·<span·class="pre">sOFF_TF15</span></code>)·which·have·properties·that·have·been·pre-calculated·using·electrophysiological·recordings·from·the·mouse·LGN·(Durant·et.·al·2016,·Billeh·et.·al·2019).</p> |
| 1163 | <p>A·combination·of·a·Gaussian·spatial·filter·and·double·cosine·temporal·filter·are·used·to·filter·the·receptive·field.</p> | 1163 | <p>A·combination·of·a·Gaussian·spatial·filter·and·double·cosine·temporal·filter·are·used·to·filter·the·receptive·field.</p> |
| 1164 | <div·class="row"><div·class="col-md-4"><p><img·alt=" | 1164 | <div·class="row"><div·class="col-md-4"><p><img·alt="3bf6a2477d6a48c2bd354629f5912013"·class="no-scaled-link"·src="_images/filternet_spat_filter.png"·style="width:·1000px;·height:·1000px;"·/></p> |
| 1165 | </div><div·class="col-md-4"><p><img·alt=" | 1165 | </div><div·class="col-md-4"><p><img·alt="64374f48c64d4e4e9de4b2484aa896e4"·class="no-scaled-link"·src="_images/filternet_temp_filter.png"·style="width:·300px;·height:·300px;"·/></p> |
| 1166 | </div></div></div> | 1166 | </div></div></div> |
| 1167 | <div·class="section"·id="parameters"> | 1167 | <div·class="section"·id="parameters"> |
| 1168 | <h3>parameters<a·class="headerlink"·href="#parameters"·title="Permalink·to·this·headline">¶</a></h3> | 1168 | <h3>parameters<a·class="headerlink"·href="#parameters"·title="Permalink·to·this·headline">¶</a></h3> |
| 1169 | <p>The·parameters·for·the·cell·are·by·default·set·in·the·.json·file·pointed·to·by·the·<code·class="docutils·literal·notranslate"><span·class="pre">dynamic_params</span></code>·parameter·are·calculated·from·extracellular·recordings·from·the·mouse·LGN·(Durand·et.·al·2016,·Billeh·et.·al,·2019).·These·parameters·may·be·over·ridden·to·be·unique·to·each·cell·by·passing·in·a·list·of·values·in·the·call·to·<code·class="docutils·literal·notranslate"><span·class="pre">add_nodes</span></code>.·For·example·to·given·every·cell·a·randomized·spontaneous·firing·rate·using·the·spont_fr·variable·(see·below)·you·would·just·add·the·following:</p> | 1169 | <p>The·parameters·for·the·cell·are·by·default·set·in·the·.json·file·pointed·to·by·the·<code·class="docutils·literal·notranslate"><span·class="pre">dynamic_params</span></code>·parameter·are·calculated·from·extracellular·recordings·from·the·mouse·LGN·(Durand·et.·al·2016,·Billeh·et.·al,·2019).·These·parameters·may·be·over·ridden·to·be·unique·to·each·cell·by·passing·in·a·list·of·values·in·the·call·to·<code·class="docutils·literal·notranslate"><span·class="pre">add_nodes</span></code>.·For·example·to·given·every·cell·a·randomized·spontaneous·firing·rate·using·the·spont_fr·variable·(see·below)·you·would·just·add·the·following:</p> |
| 1170 | <div·class="highlight-python·notranslate"><div·class="highlight"><pre><span></span><span·class="n">net</span><span·class="o">.</span><span·class="n">add_nodes</span><span·class="p">(</span>··<span·class="c1">#·add·10·simple·ON·cells</span> | 1170 | <div·class="highlight-python·notranslate"><div·class="highlight"><pre><span></span><span·class="n">net</span><span·class="o">.</span><span·class="n">add_nodes</span><span·class="p">(</span>··<span·class="c1">#·add·10·simple·ON·cells</span> |
| 1171 | ····<span·class="n">N</span><span·class="o">=</span><span·class="mi">20</span><span·class="p">,</span> | 1171 | ····<span·class="n">N</span><span·class="o">=</span><span·class="mi">20</span><span·class="p">,</span> |
| 1172 | ····<span·class="n">model_template</span><span·class="o">=</span><span·class="s1">'lgnmodel:tON'</span><span·class="p">,</span> | 1172 | ····<span·class="n">model_template</span><span·class="o">=</span><span·class="s1">'lgnmodel:tON'</span><span·class="p">,</span> |
| Offset 220, 16 lines modified | Offset 220, 16 lines modified | ||
| 220 | call·to·add_nodes(...).·There·are·also·a·number·of·special·types·(tON_TF8, | 220 | call·to·add_nodes(...).·There·are·also·a·number·of·special·types·(tON_TF8, |
| 221 | sON_TF1,·sON_TF2,·sON_TF4,·sON_TF8,·sON_TF15,·tOFF_TF1,·tOFF_TF2,·tOFF_TF4, | 221 | sON_TF1,·sON_TF2,·sON_TF4,·sON_TF8,·sON_TF15,·tOFF_TF1,·tOFF_TF2,·tOFF_TF4, |
| 222 | tOFF_TF8,·tOFF_TF15,·sOFF_TF1,·sOFF_TF2,·sOFF_TF4,·sOFF_TF8,·sOFF_TF15)·which | 222 | tOFF_TF8,·tOFF_TF15,·sOFF_TF1,·sOFF_TF2,·sOFF_TF4,·sOFF_TF8,·sOFF_TF15)·which |
| 223 | have·properties·that·have·been·pre-calculated·using·electrophysiological | 223 | have·properties·that·have·been·pre-calculated·using·electrophysiological |
| 224 | recordings·from·the·mouse·LGN·(Durant·et.·al·2016,·Billeh·et.·al·2019). | 224 | recordings·from·the·mouse·LGN·(Durant·et.·al·2016,·Billeh·et.·al·2019). |
| 225 | A·combination·of·a·Gaussian·spatial·filter·and·double·cosine·temporal·filter | 225 | A·combination·of·a·Gaussian·spatial·filter·and·double·cosine·temporal·filter |
| 226 | are·used·to·filter·the·receptive·field. | 226 | are·used·to·filter·the·receptive·field. |
| 227 | [1c90a41a81834ea7b354533b3f1e9e93] | ||
| 228 | [ | 227 | [3bf6a2477d6a48c2bd354629f5912013] |
| 228 | [64374f48c64d4e4e9de4b2484aa896e4] | ||
| 229 | ****·parameters¶·**** | 229 | ****·parameters¶·**** |
| 230 | The·parameters·for·the·cell·are·by·default·set·in·the·.json·file·pointed·to·by | 230 | The·parameters·for·the·cell·are·by·default·set·in·the·.json·file·pointed·to·by |
| 231 | the·dynamic_params·parameter·are·calculated·from·extracellular·recordings·from | 231 | the·dynamic_params·parameter·are·calculated·from·extracellular·recordings·from |
| 232 | the·mouse·LGN·(Durand·et.·al·2016,·Billeh·et.·al,·2019).·These·parameters·may | 232 | the·mouse·LGN·(Durand·et.·al·2016,·Billeh·et.·al,·2019).·These·parameters·may |
| 233 | be·over·ridden·to·be·unique·to·each·cell·by·passing·in·a·list·of·values·in·the | 233 | be·over·ridden·to·be·unique·to·each·cell·by·passing·in·a·list·of·values·in·the |
| 234 | call·to·add_nodes.·For·example·to·given·every·cell·a·randomized·spontaneous | 234 | call·to·add_nodes.·For·example·to·given·every·cell·a·randomized·spontaneous |
| 235 | firing·rate·using·the·spont_fr·variable·(see·below)·you·would·just·add·the | 235 | firing·rate·using·the·spont_fr·variable·(see·below)·you·would·just·add·the |
| Offset 1658, 15 lines modified | Offset 1658, 15 lines modified | ||
| 1658 | <img·alt="_images/tutorial_pointnet_modeling_33_0.png"·src="_images/tutorial_pointnet_modeling_33_0.png"·/> | 1658 | <img·alt="_images/tutorial_pointnet_modeling_33_0.png"·src="_images/tutorial_pointnet_modeling_33_0.png"·/> |
| 1659 | </div> | 1659 | </div> |
| 1660 | </div> | 1660 | </div> |
| 1661 | </div> | 1661 | </div> |
| 1662 | <div·class="section"·id="Perturbation-simulations"> | 1662 | <div·class="section"·id="Perturbation-simulations"> |
| 1663 | <h3>Perturbation·simulations<a·class="headerlink"·href="#Perturbation-simulations"·title="Permalink·to·this·headline">¶</a></h3> | 1663 | <h3>Perturbation·simulations<a·class="headerlink"·href="#Perturbation-simulations"·title="Permalink·to·this·headline">¶</a></h3> |
| 1664 | <p>A·common·use·case·is·to·mimick·a·network·where·the·firing·rate·of·select·cells·are·being·depressed·or·stimulated·using·current·clamps·or·optogenetic·methods.·The·best·way·to·do·this·is·by·applying·a·current·clamp·in·a·similar·manner·used·in·<a·class="reference·external"·href="http://localhost:32000/notebooks/Workspace/bmtk/docs/tutorial/01_single_cell_clamped.ipynb">bionet</a>.</p> | 1664 | <p>A·common·use·case·is·to·mimick·a·network·where·the·firing·rate·of·select·cells·are·being·depressed·or·stimulated·using·current·clamps·or·optogenetic·methods.·The·best·way·to·do·this·is·by·applying·a·current·clamp·in·a·similar·manner·used·in·<a·class="reference·external"·href="http://localhost:32000/notebooks/Workspace/bmtk/docs/tutorial/01_single_cell_clamped.ipynb">bionet</a>.</p> |
| 1665 | <p>The·point_120cells·network·in·the·bmtk·examples·consists·of·120·recurrently·connected·excitatory·and·inhibitory·cells·with·randomized·inputs.·Normally·the·results·without·any·type·of·perturbations·will·look·as·follows:·<img·alt=" | 1665 | <p>The·point_120cells·network·in·the·bmtk·examples·consists·of·120·recurrently·connected·excitatory·and·inhibitory·cells·with·randomized·inputs.·Normally·the·results·without·any·type·of·perturbations·will·look·as·follows:·<img·alt="5fb2a2d79f714b4db25fe769bed98a2b"·src="_images/raster_120cells_orig.png"·/></p> |
| 1666 | <p>To·artifically·excite·some·of·the·cells·we·can·open·the·config.json·file·and·add·the·following·section·to·the·“inputs”:</p> | 1666 | <p>To·artifically·excite·some·of·the·cells·we·can·open·the·config.json·file·and·add·the·following·section·to·the·“inputs”:</p> |
| 1667 | <div·class="highlight-json·notranslate"><div·class="highlight"><pre><span></span><span·class="p">{</span> | 1667 | <div·class="highlight-json·notranslate"><div·class="highlight"><pre><span></span><span·class="p">{</span> |
| 1668 | ··<span·class="nt">"exc_perturbation"</span><span·class="p">:</span>·<span·class="p">{</span> | 1668 | ··<span·class="nt">"exc_perturbation"</span><span·class="p">:</span>·<span·class="p">{</span> |
| 1669 | ····<span·class="nt">"input_type"</span><span·class="p">:</span>·<span·class="s2">"current_clamp"</span><span·class="p">,</span> | 1669 | ····<span·class="nt">"input_type"</span><span·class="p">:</span>·<span·class="s2">"current_clamp"</span><span·class="p">,</span> |
| 1670 | ····<span·class="nt">"module"</span><span·class="p">:</span>·<span·class="s2">"IClamp"</span><span·class="p">,</span> | 1670 | ····<span·class="nt">"module"</span><span·class="p">:</span>·<span·class="s2">"IClamp"</span><span·class="p">,</span> |
| 1671 | ····<span·class="nt">"node_set"</span><span·class="p">:</span>·<span·class="p">{</span> | 1671 | ····<span·class="nt">"node_set"</span><span·class="p">:</span>·<span·class="p">{</span> |
| 1672 | ······<span·class="nt">"population"</span><span·class="p">:</span>·<span·class="s2">"cortex"</span><span·class="p">,</span> | 1672 | ······<span·class="nt">"population"</span><span·class="p">:</span>·<span·class="s2">"cortex"</span><span·class="p">,</span> |
| Offset 1701, 15 lines modified | Offset 1701, 15 lines modified | ||
| 1701 | ····<span·class="nt">"amp"</span><span·class="p">:</span>·<span·class="mf">-230.0</span><span·class="p">,</span> | 1701 | ····<span·class="nt">"amp"</span><span·class="p">:</span>·<span·class="mf">-230.0</span><span·class="p">,</span> |
| 1702 | ····<span·class="nt">"delay"</span><span·class="p">:</span>·<span·class="mf">1.0</span><span·class="p">,</span> | 1702 | ····<span·class="nt">"delay"</span><span·class="p">:</span>·<span·class="mf">1.0</span><span·class="p">,</span> |
| 1703 | ····<span·class="nt">"duration"</span><span·class="p">:</span>·<span·class="mf">3000.0</span> | 1703 | ····<span·class="nt">"duration"</span><span·class="p">:</span>·<span·class="mf">3000.0</span> |
| 1704 | ··<span·class="p">}</span> | 1704 | ··<span·class="p">}</span> |
| 1705 | <span·class="p">}</span> | 1705 | <span·class="p">}</span> |
| 1706 | </pre></div> | 1706 | </pre></div> |
| 1707 | </div> | 1707 | </div> |
| 1708 | <p>After·we·rerun·the·simulation:·<img·alt="52 | 1708 | <p>After·we·rerun·the·simulation:·<img·alt="e52b195509e74a8e80b1dc7216fb0362"·src="_images/raster_120cells_perturbed.png"·/></p> |
| 1709 | <div·class="nbinput·nblast·docutils·container"> | 1709 | <div·class="nbinput·nblast·docutils·container"> |
| 1710 | <div·class="prompt·highlight-none·notranslate"><div·class="highlight"><pre><span></span>[·]: | 1710 | <div·class="prompt·highlight-none·notranslate"><div·class="highlight"><pre><span></span>[·]: |
| 1711 | </pre></div> | 1711 | </pre></div> |
| 1712 | </div> | 1712 | </div> |
| 1713 | <div·class="input_area·highlight-ipython3·notranslate"><div·class="highlight"><pre> | 1713 | <div·class="input_area·highlight-ipython3·notranslate"><div·class="highlight"><pre> |
| 1714 | <span></span> | 1714 | <span></span> |
| 1715 | </pre></div> | 1715 | </pre></div> |
| Offset 419, 15 lines modified | Offset 419, 15 lines modified | ||
| 419 | A·common·use·case·is·to·mimick·a·network·where·the·firing·rate·of·select·cells | 419 | A·common·use·case·is·to·mimick·a·network·where·the·firing·rate·of·select·cells |
| 420 | are·being·depressed·or·stimulated·using·current·clamps·or·optogenetic·methods. | 420 | are·being·depressed·or·stimulated·using·current·clamps·or·optogenetic·methods. |
| 421 | The·best·way·to·do·this·is·by·applying·a·current·clamp·in·a·similar·manner·used | 421 | The·best·way·to·do·this·is·by·applying·a·current·clamp·in·a·similar·manner·used |
| 422 | in·bionet. | 422 | in·bionet. |
| 423 | The·point_120cells·network·in·the·bmtk·examples·consists·of·120·recurrently | 423 | The·point_120cells·network·in·the·bmtk·examples·consists·of·120·recurrently |
| 424 | connected·excitatory·and·inhibitory·cells·with·randomized·inputs.·Normally·the | 424 | connected·excitatory·and·inhibitory·cells·with·randomized·inputs.·Normally·the |
| 425 | results·without·any·type·of·perturbations·will·look·as·follows: | 425 | results·without·any·type·of·perturbations·will·look·as·follows: |
| 426 | [ | 426 | [5fb2a2d79f714b4db25fe769bed98a2b] |
| 427 | To·artifically·excite·some·of·the·cells·we·can·open·the·config.json·file·and | 427 | To·artifically·excite·some·of·the·cells·we·can·open·the·config.json·file·and |
| 428 | add·the·following·section·to·the·âinputsâ: | 428 | add·the·following·section·to·the·âinputsâ: |
| 429 | { | 429 | { |
| 430 | ··"exc_perturbation":·{ | 430 | ··"exc_perturbation":·{ |
| 431 | ····"input_type":·"current_clamp", | 431 | ····"input_type":·"current_clamp", |
| 432 | ····"module":·"IClamp", | 432 | ····"module":·"IClamp", |
| 433 | ····"node_set":·{ | 433 | ····"node_set":·{ |
| Offset 462, 15 lines modified | Offset 462, 15 lines modified | ||
| 462 | ······"node_ids":·[40,·41,·42,·43,·44,·45,·46,·47,·48,·49] | 462 | ······"node_ids":·[40,·41,·42,·43,·44,·45,·46,·47,·48,·49] |
| 463 | ····}, | 463 | ····}, |
| 464 | ····"amp":·-230.0, | 464 | ····"amp":·-230.0, |
| 465 | ····"delay":·1.0, | 465 | ····"delay":·1.0, |
| 466 | ····"duration":·3000.0 | 466 | ····"duration":·3000.0 |
| 467 | ··} | 467 | ··} |
| 468 | } | 468 | } |
| 469 | After·we·rerun·the·simulation:·[52 | 469 | After·we·rerun·the·simulation:·[e52b195509e74a8e80b1dc7216fb0362] |
| 470 | [·]: | 470 | [·]: |
| 471 | ****·Contents·**** | 471 | ****·Contents·**** |
| 472 | ····*·Installation_Guide | 472 | ····*·Installation_Guide |
| 473 | ····*·Building_Networks | 473 | ····*·Building_Networks |
| 474 | ····*·Simulation_Engines | 474 | ····*·Simulation_Engines |
| 475 | ··········o·BioNet | 475 | ··········o·BioNet |
| 476 | ··········o·PointNet | 476 | ··········o·PointNet |