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typos and minor changes to handouts
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flier/eppy-handout.tex

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%_________________________________neo_______________________________________
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\ndproject{Neo}{http://packages.python.org/neo}{neo_logo.pdf}{.4}{-0.25em}{-5em}
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Neo is a package provides a common model for representing
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Neo provides a common model for representing
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electrophysiology data in Python. It provides I/O for reading a wide
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range of neurophysiology file formats, including Spike2,
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NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and for
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range of neurophysiology file formats (Spike2,
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NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt) and for
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writing to a subset of these formats plus non-proprietary formats
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including HDF5.
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% lightweight a dependency as possible, Neo is deliberately limited to represention of data,
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% with no functions for data analysis or visualization.
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Neo implements a hierarchical data model well adapted to intracellular
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Neo implements a hierarchical data model well-adapted to intracellular
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and extracellular electrophysiology and EEG data with support for
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multi-electrodes (for example tetrodes). Neo's data objects build on
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multi-electrodes (e.g., tetrodes). Neo's data objects build on
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the \href{http://pypi.python.org/pypi/quantities}{quantities} package,
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which in turn builds on \href{http://www.numpy.org}{NumPy} by adding
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support for physical dimensions. Thus Neo objects behave just like
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normal NumPy arrays, but with additional metadata, checks for
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support for physical dimensions. Thus Neo objects behave like
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normal NumPy arrays but with additional metadata, checks for
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dimensional consistency and automatic unit conversion.
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A project with similar aims but for neuroimaging file formats is
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OpenElectrophy is build on top of neo. It provides
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\begin{itemize}[nolistsep,topsep=0em,leftmargin=1pc]
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\item Powerfull GUI
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\item Powerful GUI
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\item Collection of methods for spike sorting
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\item Wavelet method for analysing transient oscillations in LFP
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\item Wavelet method for analyzing transient oscillations in LFP
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\item Customisable database to organize datasets
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\end{itemize}
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\vspace{0.5em} %some additional spacing
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LFPy is a Python module for simulation of extracellular electrical
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potentials evoked by activity of multi-compartment model neurons.
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LFPy runs on top of the NEURON-simulator, using the Python interface
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that is included (\url{http://www.neuron.yale.edu}).
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LFPy runs on top of the NEURON-simulator, using the included Python interface
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(\url{http://www.neuron.yale.edu}).
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LFPy provides:
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\begin{itemize}[nolistsep, topsep=0em, leftmargin=1pc]
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\item A forward modeling scheme for calculating extracellular potentials from compartmental membrane currents in an infinite homogeneous linear extracellular medium.
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\item Simple to use Python-classes for setting up the cells, synapses and recording electrodes.
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\item Simple to use Python-classes for setting up cells, synapses and recording electrodes.
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\item Easy to use scripting capabilities thanks to NEURON and the Python programming environment.
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\item Functionality to employ or specify biophysically detailed model neurons, add stimulus, and perform simultaneous simulation of the model cell responses and extracellular potentials.
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\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.
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\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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\end{itemize}
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%\includegraphics[width=0.3\columnwidth]{../pics/psychopy_logo.pdf}
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%\end{figure}
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Visualise and quantify electrophysiological data.
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Visualize and quantify electrophysiological data.
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\begin{itemize}[nolistsep,topsep=0em,leftmargin=1pc]
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\item With a focus on patch-clamp recordings
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\item Supports most standard patch-clamp file types
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\item Embedded Python shell
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\item Measure action potential, EPSC and EPSP kinetics
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\item Extract spontaneous and evoked events
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\item Measures action potential, EPSC and EPSP kinetics
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\item Extracts spontaneous and evoked events
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\item Successfully used in many publications for >\,5 years
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\end{itemize}
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% Your favorite screenshot placed under ../pics/

flier/nipy-handout.tex

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\item Databasing capabilities
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\item Massive computation facilities using Soma-workflow
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\item Open environment, with many toolboxes
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\item Specialized toolboxes for T1 MRI processing, sulci ang gyri morphometry,
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\item Specialized toolboxes for T1 MRI processing, sulci and gyri morphometry,
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diffusion imaging and fibers tracking, surfacic and structural analysis,
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3D histology\ldots
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\item Links with other software like SPM, FSL, FreeSurfer, or CIVET

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