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Electrophysiology File Converters to HDF5
Internal Dataset

UID: 23

Author(s): Horn, Charles C.*+, Rosenberg, David M. * Corresponding Author + University of Pittsburgh Author
Description
This Github repository contains Python code to convert electrophysiology data files to Numpy arrays and save them to HDF5. The package contains example Spike2 data, a Jupyter notebook, and Python code to be executed within the notebook.
Keywords
Electrophysiology
File conversion (Computer science)
Software
Access via Github

Python script, Jupyter notebook, and example Spike2 data

Access Restrictions
Free to all
Access Instructions
Download via Github. Requires Python, Jupyter (required for using the notebook to run the Python script), Numpy, Matplotlib, Neo (these converters make heavy use of the Neo package). MIT license requires a copyright notice and permission notice to be included in all copies or substantial portions of the software.
Associated Publications
Rosenberg DM, Horn CC. Neurophysiological analytics for all! Free open-source software tools for documenting, analyzing, visualizing, and sharing using electronic notebooks. J Neurophysiol. 2016 Aug 1;116(2):252-62. doi: 10.1152/jn.00137.2016. Epub 2016 Apr 20. PMID: 27098025; PMCID: PMC4969392.
Data Type
Electrophysiological
Software Used
Jupyter Notebook

App to create, edit, and run documents containing computer code and rich text.

Matplotlib

Python 2D plotting library.

Neo

Python module for loading and saving multiple electrophysiology data formats.

NumPy

Python scientific computing package.

Spike2

Multi-channel continuous data acquisition and analysis package

Dataset Format(s)
PY (.py), Spike2 data (.smr, .smrx), IPYNB (.ipynb), HDF5 (.h5, .hdf5, .he5)
Resource Type(s)
Software
Dataset Size
2.41 MB
Grant Support
U18 EB021772/NIBIB
Data Catalog Record Updated
2021-02-09

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