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Niru Maheswaranathan committed Dec 1, 2016
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title: 'Pyret: A Python package for analysis of neurophysiology data'
tags:
- neuroscience
- sensory
- retina
authors:
- name: Benjamin Naecker
orcid: 0000-0002-7525-1635
affiliation: 1
affiliation: 1
- name: Niru Maheswaranathan
orcid: 0000-0002-3946-4705
affiliation: 1
- name: Surya Ganguli
affiliation: 2, 3
- name: Stephen Baccus
affiliation: 3
affiliations:
- name: Neurosciences Graduate Program, Stanford University
index: 1
index: 1
- name: Department of Applied Physics, Stanford University
index: 2
- name: Department of Neurobiology, Stanford University
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# Summary

The Pyret package contains tools for analyzing neural electrophysiology data. It focuses
on applications in sensory neuroscience, broadly construed as any experiment in which
one would like to characterize neural responses to a sensory stimulus. Pyret contains
methods for manipulating spike trains (e.g. binning and smoothing); pre-processing
experimental stimuli (e.g. resampling); computing spike-triggered averages and
ensembles [@Schwartz2006]; estimating linear-nonlinear cascade models
[@Chichilnisky2001,@Pedregosa2011] to predict neural responses to different stimuli;
as well as a suite of visualization tools for all the above.
The *pyret* package contains tools for analyzing neural electrophysiology data.
It focuses on applications in sensory neuroscience, broadly construed as any experiment in which one would like to characterize neural responses to a sensory stimulus.
Pyret contains methods for manipulating spike trains (e.g. binning and smoothing), pre-processing experimental stimuli (e.g. resampling), computing spike-triggered averages and ensembles [@pchwartz2006], estimating linear-nonlinear cascade models to predict neural responses to different stimuli [@phichilnisky2001], part of which follows the scikit-learn API [@pedregosa2011], as well as a suite of visualization tools for all the above.
We designed *pyret* to be simple, robust, and efficient with broad applicability across a range of sensory neuroscience analyses.

Full API documentation and a short tutorial can be found at [http://pyret.readthedocs.io/](http://pyret.readthedocs.io/)

# References

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