alandegenhart / neuropy

Python toolbox for neural analysis

NeuroPy: a Python toolbox for the analysis of neural data

Note: this package is in active development and use and is likely to change dramatically without notice.

This package contains a collection of Python code for the analysis of neural data. It was initially created while I was a postdoc at Carnegie Mellon University to aid in the analysis of intracortical recordings during brain-computer interface (BCI) tasks. After moving to the Allen Institute I continued to use and develop this code base, adding functionality for interacting with Allen Institute Brain Observatory data.

Installation

I recommend installing this package in 'development' mode via pip. After cloning the repository, navigate to the root directory of the package and run: pip install -e .. I generally prefer using Anaconda for environment management, though this should also work with venv.

Highlights (i.e., things that might be useful to others):

• analysis/stiefel.py : code to perform optimization over the stiefel manifold. Allows the user to create subclasses for new objective functions.
• dimred.py : module for dimensionality-reduction analyses. Contains a Python implementation of Factor Analysis based on Expectation Maximization (EM).
• pbstools.py : module for running code on the AIBS cluster (PBS/Moab).

Brief description of all modules

Note: this list is not currently up to date.

• analysis : general analysis sub-package
  • gpfa.py : module for processing GPFA (Gaussian Process Factor Analysis) data
  • math.py : currently a catch-all for math functions without a home. Contains an implementation of Fisher's LDA. [deprecated]
  • stiefel.py : code to perform optimization over the stiefel manifold. Allows the user to create subclasses for new objective functions.
• array.py : helper functions for interacting with array data
• decomposition.py : outdated code for performing dimensionality-reduction analyses. Will eventually be merged with dimred.py. [deprecated]
• dev.py : contains functions for interacting with ABIS Brain Observatory data.
• dimred.py : module for dimensionality-reduction analyses. Contains a Python implementation of Factor Analysis based on Expectation Maximization (EM).
• mathutil.py : another math catch-all. Supersedes analysis/math.py, which will eventually be removed.
• movie.py : code for interacting with AIBS Brain Observatory natural movie data.
• pbstools.py : module for running code on the AIBS cluster (PBS/Moab).
• plot.py : useful plotting functions. Some may be analysis-specific currently.
• preprocessing.py : preprocessing code for AIBS Brain Observatory data.
• temp.py : temporary location for code without a home. Currently contains a lot of functions specific to a project from my postdoc that will be removed.
• util : utilities sub-package
  • convertmat.py : module for loading MATLAB HDF5 data into Python using Pandas
• utilities : AIBS-related utilities.