nelpy 0.0.95

Neuroelectrophysiology object model and data analysis in Python.

Neuroelectrophysiology object model and analysis in Python.

Overview

Nelpy (NeuroELectroPhysiologY) is an open source package for analysis of neuroelectrophysiology data arising (primarily) from extracellular electrode recordings during neuroscience experiments. The functionality of this package includes:

• item 1

• item 2

• hidden Markov model analysis of neural activity

• basic data exploration and visualization operating directly on the core nelpy objects

Quick example

Let’s give it a try. Create a SpikeTrainArray:

>>> import nelpy as nel  # main nelpy imports
>>> import nelpy.plotting as npl  # optional plotting imports
>>> spike_times = np.array([1, 2, np.nan, 4, 5])

Do something:

>>> st.n_units
3.0

Related work and inspiration

Nelpy drew heavy inspiration from the python-vdmlab package from the van der Meer lab at Dartmouth College (https://github.com/vandermeerlab), which was created by Emily Irvine (https://github.com/emirvine). It is also inspired by the neuralensemble.org NEO project (http://neo.readthedocs.io).

Scope of this work

The nelpy object model is expected to be quite similar to the python-vdmlab object model, which in turn has significant overlap with neuralensemble.org’s neo model. However, the nelpy object model extends the former by making binned data first class citizens, and by changing the API for indexing and extracting subsets of data, as well as making “functional support” an integral part of the model. It (nelpy) is currently simpler and less comprehensive than neo, and specifically lacks in terms of physical units and complex object hierarchies and nonlinear relationships. However, nelpy again makes binned data a core object, and nelpy further aims to add additional analysis code including filtering, smoothing, position analysis, subsampling, interpolation, spike rate estimation, spike generation / synthesis, ripple detection, Bayesian decoding, and so on. In short, nelpy is more than just an object model, but the nelpy core is designed to be a flexible, readable, yet powerful object model for neuroelectrophysiology.

Installation

The easiest way to install Nelpy is to use pip. From the terminal, run:

pip install nelpy

Alternatively, you can install the latest version of nelpy by running the following commands:

git clone https://github.com/eackermann/nelpy.git
cd nelpy
python setup.py [install, develop]

where the develop argument should be used if you want to modify the code.

Where

download	https://pypi.python.org/pypi/nelpy
docs	coming soon!
code	https://github.com/eackermann/nelpy

License

Nelpy is distributed under the MIT license. See the LICENSE file for details.