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1 | 1 |
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2 | 2 | \include{common-handout}
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3 | 3 |
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| 4 | +\raggedcolumns |
| 5 | + |
4 | 6 | \hypersetup{
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5 | 7 | pdftitle={Python in Electrophysiology},
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6 | 8 | }
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133 | 135 |
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134 | 136 | %___________________________________________________________________________
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135 | 137 |
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| 138 | + |
136 | 139 | %___________________________________________________________________________
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137 | 140 | \ndsection{Metadata Management}%
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138 | 141 |
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149 | 152 | \includegraphics[width=\columnwidth]{odml_editor_screenshot.png}
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150 | 153 |
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151 | 154 | \ndcite{Grewe J, Wachtler T, Benda J (2011) A bottom-up approach to data annotation in neurophysiology. Front. Neuroinform. 5:16. doi:~10.3389/fninf.2011.00016\\}
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152 |
| -\ndsection{Data Archiving} |
153 |
| -\ndsection{Experimentation Control} |
| 155 | +%\ndsection{Data Archiving} |
| 156 | +%\ndsection{Experimentation Control} |
| 157 | + |
| 158 | +\ndsection{Simulation Tools} |
| 159 | + |
| 160 | +%________________________LFPy_______________________________________________ |
| 161 | + |
| 162 | +\ndproject{LFPy}{http://compneuro.umb.no/LFPy}{lfpy_logo.pdf}{.3}{-0.25em}{-3em} |
| 163 | + |
| 164 | +\vspace{0.5em} %some additional spacing |
| 165 | +LFPy is a Python module for simulation of extracellular electrical |
| 166 | +potentials evoked by activity of multi-compartment model neurons. |
| 167 | +LFPy runs on top of the NEURON-simulator, using the Python interface |
| 168 | +that is included (\url{http://www.neuron.yale.edu}). |
| 169 | + |
| 170 | +LFPy provides: |
| 171 | +\begin{itemize}[nolistsep, topsep=0em, leftmargin=1pc] |
| 172 | +\item A forward modeling scheme for calculating extracellular potentials from compartmental membrane currents in an infinite homogeneous linear extracellular medium. |
| 173 | +\item Simple to use Python-classes for setting up the cells, synapses and recording electrodes. |
| 174 | +\item Easy to use scripting capabilities thanks to NEURON and the Python programming environment. |
| 175 | +\item Functionality to employ or specify biophysically detailed model neurons, add stimulus, and perform simultaneous simulation of the model cell responses and extracellular potentials. |
| 176 | +\item Support for common formats for reconstructed neuronal morphologies, allowing use of publicly available 3D-reconstructions (e.g., \url{http://www.neuromorpho.org}). |
| 177 | +\end{itemize} |
| 178 | + |
| 179 | + |
| 180 | +%___________________________________________________________________________ |
| 181 | + |
| 182 | +\columnbreak |
154 | 183 | \ndsection{Analysis}%
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155 | 184 |
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156 | 185 | %________________________Stimfit____________________________________________
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180 | 209 | % Selected set of citations, Here is an example:
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181 | 210 | % Working on a manuscript right now ;-)
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182 | 211 |
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| 212 | +\columnbreak |
| 213 | + |
183 | 214 | %________________________Spyke Viewer_______________________________________
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184 | 215 |
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185 | 216 | % Your logo placed under ../pics called as <project>_logo.svg
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223 | 254 | %___________________________________________________________________________
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224 | 255 |
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225 | 256 | \includegraphics[width=\columnwidth]{spikesort_screenshot.png}
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226 |
| -\ndsection{Closed-loop Frameworks}% |
| 257 | +%\ndsection{Closed-loop Frameworks}% |
227 | 258 |
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228 | 259 | %___________________________________________________________________________
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229 | 260 |
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230 | 261 |
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231 |
| -\ndsection{Simulation Tools} |
232 |
| - |
233 |
| -%________________________LFPy_______________________________________________ |
234 |
| - |
235 |
| -\ndproject{LFPy}{http://compneuro.umb.no/LFPy}{lfpy_logo.pdf}{.3}{-0.25em}{-3em} |
236 |
| - |
237 |
| -\vspace{0.5em} %some additional spacing |
238 |
| -LFPy is a Python module for simulation of extracellular electrical |
239 |
| -potentials evoked by activity of multi-compartment model neurons. |
240 |
| -LFPy runs on top of the NEURON-simulator, using the Python interface |
241 |
| -that is included (\url{http://www.neuron.yale.edu}). |
242 |
| - |
243 |
| -LFPy provides: |
244 |
| -\begin{itemize}[nolistsep, topsep=0em, leftmargin=1pc] |
245 |
| -\item A forward modeling scheme for calculating extracellular potentials from compartmental membrane currents in an infinite homogeneous linear extracellular medium. |
246 |
| -\item Simple to use Python-classes for setting up the cells, synapses and recording electrodes. |
247 |
| -\item Easy to use scripting capabilities thanks to NEURON and the Python programming environment. |
248 |
| -\item Functionality to employ or specify biophysically detailed model neurons, add stimulus, and perform simultaneous simulation of the model cell responses and extracellular potentials. |
249 |
| -\item Support for common formats for reconstructed neuronal morphologies, allowing use of publicly available 3D-reconstructions (e.g., \url{http://www.neuromorpho.org}). |
250 |
| -\end{itemize} |
251 |
| - |
252 |
| - |
253 |
| -%___________________________________________________________________________ |
254 |
| - |
255 |
| - |
256 |
| - |
257 | 262 |
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258 | 263 |
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259 | 264 | \end{multicols}
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