AP halfwidth measurement for NEURON
||This simple example shows how to measure half width of Action Potentials (in milliseconds).
Average a data file to make a smaller data file
||This utility will read the file specified in the hoc program and write the file specified in the hoc program with blocks of the input file averaged into a single time point. (See top of hoc file for settings) This is a very simple program!
Cross Correlation Tool
||This GUI tool wraps the Vector.correl function
http://www.neuron.yale.edu/neuron/docs/help/neuron/general/classes/vector/vect2.html#$Since Vector.correl is implemented using the fast fourier transform
this tool interpolates the vectors in the domain tbegin to tend onto
a grid with number of points equal to a power of 2. To do this an
"actual dt" is selected which is near the "nominal dt" grid spacing and
satisfies (tend-tbegin)/"actual dt" = 2^n where n is an integer.
PANDORA Neural Analysis Toolbox
||<p>PANDORA is a Matlab Toolbox that makes database management accessible from your electrophysiology project.
<p>PANDORA works by extracting user-defined characteristics from raw neural data (e.g., voltage traces) and creating numerical database tables from them. These tables can then be subjected to further analyses, such as invariant effects, statistical, correlation, and principal components. Publication-ready plots can be produced with an embedded plotting system.
<p> PANDORA's features are:
<li>Works offline within Matlab;
<li>requires no external software;
<li>is object oriented and allows easy extensions;
<li>can easily tie with existing Matlab scripts;
<li>can query a database as in SQL.
<p>See <a href="http://software.incf.org/software/pandora">the PANDORA website</a> for finding documentation and the latest version of the toolbox.
Sample Entropy (SampEn) method (Neymotin et al. 2010)
||"... To determine the complexity of the EEG time
series, we calculated the sample entropy (SampEn) .... SampEn is the negative natural logarithm of an
estimate of the conditional probability that subseries (epochs) of
length m-1 that match pointwise within a tolerance r also match
at the mth point. ..."
SimTracker - Parallel NEURON network model simulation management & analysis
||The SimTracker tool streamlines the entire modeling process, from code writing/versioning and simulation design to execution of simulations on a variety of machines (local, remote supercomputer, NSG) to organization and analysis of simulation results. It also provides tools to:
- characterize model components (cells, synapses, ion channels) in experimentalist-friendly ways
- read in experimental data and fit model components using that data (in conjunction with NEURON's Multiple Run Fitter)
- Explore the parameter space of the model
- Share model specifications and results online in an interactive manner, as an alternative to placing all the figures/tables into a supplemental PDF for a publication, although LaTeX code for a PDF can also be generated.