|
1 | 1 |
|
2 | 2 | \include{common-handout} |
3 | 3 |
|
| 4 | +\raggedcolumns |
| 5 | + |
4 | 6 | \hypersetup{ |
5 | 7 | pdftitle={Python in Electrophysiology}, |
6 | 8 | } |
|
133 | 135 |
|
134 | 136 | %___________________________________________________________________________ |
135 | 137 |
|
| 138 | + |
136 | 139 | %___________________________________________________________________________ |
137 | 140 | \ndsection{Metadata Management}% |
138 | 141 |
|
|
149 | 152 | \includegraphics[width=\columnwidth]{odml_editor_screenshot.png} |
150 | 153 |
|
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\\} |
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}% |
155 | 184 |
|
156 | 185 | %________________________Stimfit____________________________________________ |
|
180 | 209 | % Selected set of citations, Here is an example: |
181 | 210 | % Working on a manuscript right now ;-) |
182 | 211 |
|
| 212 | +\columnbreak |
| 213 | + |
183 | 214 | %________________________Spyke Viewer_______________________________________ |
184 | 215 |
|
185 | 216 | % Your logo placed under ../pics called as <project>_logo.svg |
|
223 | 254 | %___________________________________________________________________________ |
224 | 255 |
|
225 | 256 | \includegraphics[width=\columnwidth]{spikesort_screenshot.png} |
226 | | -\ndsection{Closed-loop Frameworks}% |
| 257 | +%\ndsection{Closed-loop Frameworks}% |
227 | 258 |
|
228 | 259 | %___________________________________________________________________________ |
229 | 260 |
|
230 | 261 |
|
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 |
|
258 | 263 |
|
259 | 264 | \end{multicols} |
|
0 commit comments