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91 | 91 | %_________________________________neo_______________________________________
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92 | 92 | \ndproject{Neo}{http://packages.python.org/neo}{neo_logo.pdf}{.4}{-0.25em}{-5em}
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93 | 93 |
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94 |
| -Neo is a package provides a common model for representing |
| 94 | +Neo provides a common model for representing |
95 | 95 | electrophysiology data in Python. It provides I/O for reading a wide
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96 |
| -range of neurophysiology file formats, including Spike2, |
97 |
| -NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and for |
| 96 | +range of neurophysiology file formats (Spike2, |
| 97 | +NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt) and for |
98 | 98 | writing to a subset of these formats plus non-proprietary formats
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99 | 99 | including HDF5.
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100 | 100 |
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104 | 104 | % lightweight a dependency as possible, Neo is deliberately limited to represention of data,
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105 | 105 | % with no functions for data analysis or visualization.
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106 | 106 |
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107 |
| -Neo implements a hierarchical data model well adapted to intracellular |
| 107 | +Neo implements a hierarchical data model well-adapted to intracellular |
108 | 108 | and extracellular electrophysiology and EEG data with support for
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109 |
| -multi-electrodes (for example tetrodes). Neo's data objects build on |
| 109 | +multi-electrodes (e.g., tetrodes). Neo's data objects build on |
110 | 110 | the \href{http://pypi.python.org/pypi/quantities}{quantities} package,
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111 | 111 | which in turn builds on \href{http://www.numpy.org}{NumPy} by adding
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112 |
| -support for physical dimensions. Thus Neo objects behave just like |
113 |
| -normal NumPy arrays, but with additional metadata, checks for |
| 112 | +support for physical dimensions. Thus Neo objects behave like |
| 113 | +normal NumPy arrays but with additional metadata, checks for |
114 | 114 | dimensional consistency and automatic unit conversion.
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115 | 115 |
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116 | 116 | A project with similar aims but for neuroimaging file formats is
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125 | 125 | OpenElectrophy is build on top of neo. It provides
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126 | 126 |
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127 | 127 | \begin{itemize}[nolistsep,topsep=0em,leftmargin=1pc]
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128 |
| -\item Powerfull GUI |
| 128 | +\item Powerful GUI |
129 | 129 | \item Collection of methods for spike sorting
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130 |
| -\item Wavelet method for analysing transient oscillations in LFP |
| 130 | +\item Wavelet method for analyzing transient oscillations in LFP |
131 | 131 | \item Customisable database to organize datasets
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132 | 132 | \end{itemize}
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133 | 133 |
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164 | 164 | \vspace{0.5em} %some additional spacing
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165 | 165 | LFPy is a Python module for simulation of extracellular electrical
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166 | 166 | potentials evoked by activity of multi-compartment model neurons.
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167 |
| -LFPy runs on top of the NEURON-simulator, using the Python interface |
168 |
| -that is included (\url{http://www.neuron.yale.edu}). |
| 167 | +LFPy runs on top of the NEURON-simulator, using the included Python interface |
| 168 | +(\url{http://www.neuron.yale.edu}). |
169 | 169 |
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170 | 170 | LFPy provides:
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171 | 171 | \begin{itemize}[nolistsep, topsep=0em, leftmargin=1pc]
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172 | 172 | \item A forward modeling scheme for calculating extracellular potentials from compartmental membrane currents in an infinite homogeneous linear extracellular medium.
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173 |
| -\item Simple to use Python-classes for setting up the cells, synapses and recording electrodes. |
| 173 | +\item Simple to use Python-classes for setting up cells, synapses and recording electrodes. |
174 | 174 | \item Easy to use scripting capabilities thanks to NEURON and the Python programming environment.
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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. |
| 175 | +\item Functionality to employ or specify biophysically detailed model neurons, add a stimulus, and perform a simultaneous simulation of the model cell responses and extracellular potentials. |
176 | 176 | \item Support for common formats for reconstructed neuronal morphologies, allowing use of publicly available 3D-reconstructions (e.g., \url{http://www.neuromorpho.org}).
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177 | 177 | \end{itemize}
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178 | 178 |
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193 | 193 | %\includegraphics[width=0.3\columnwidth]{../pics/psychopy_logo.pdf}
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194 | 194 | %\end{figure}
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195 | 195 |
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196 |
| -Visualise and quantify electrophysiological data. |
| 196 | +Visualize and quantify electrophysiological data. |
197 | 197 | \begin{itemize}[nolistsep,topsep=0em,leftmargin=1pc]
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198 | 198 | \item With a focus on patch-clamp recordings
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199 | 199 | \item Supports most standard patch-clamp file types
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200 | 200 | \item Embedded Python shell
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201 |
| -\item Measure action potential, EPSC and EPSP kinetics |
202 |
| -\item Extract spontaneous and evoked events |
| 201 | +\item Measures action potential, EPSC and EPSP kinetics |
| 202 | +\item Extracts spontaneous and evoked events |
203 | 203 | \item Successfully used in many publications for >\,5 years
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204 | 204 | \end{itemize}
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205 | 205 | % Your favorite screenshot placed under ../pics/
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