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Automatically convert neurophysiology data to NWB

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Table of Contents

About

NeuroConv is a Python package for converting neurophysiology data in a variety of proprietary formats to the Neurodata Without Borders (NWB) standard.

Features:

  • Reads data from 40 popular neurophysiology data formats and writes to NWB using best practices.
  • Extracts relevant metadata from each format.
  • Handles large data volume by reading datasets piece-wise.
  • Minimizes the size of the NWB files by automatically applying chunking and lossless compression.
  • Supports ensembles of multiple data streams, and supports common methods for temporal alignment of streams.

Installation

We always recommend installing and running Python packages in a clean environment. One way to do this is via conda environments:

conda create --name <give the environment a name> --python <choose a version of Python to use>
conda activate <environment name>

To install the latest stable release of neuroconv though PyPI, run:

pip install neuroconv

To install the current unreleased main branch (requires git to be installed in your environment, such was via conda install git), run:

pip install git+https://github.com/catalystneuro/neuroconv.git@main

NeuroConv also supports a variety of extra dependencies that can be specified inside square brackets, such as

pip install "neuroconv[openephys, dandi]"

which will then install extra dependencies related to reading OpenEphys data as well as the usage of the DANDI CLI (such as automatic upload to the DANDI Archive).

You can read more about these options in the main installation guide.

Documentation

See our ReadTheDocs page for full documentation, including a gallery of all supported formats.

License

NeuroConv is distributed under the BSD3 License. See LICENSE for more information.

Project links

Key dates

PyPI data
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  • Released:
Newer release available (0.10.2)

3 maintainers

PyPI data
Data sourced directly from PyPI's database.
Avatar for bendichter from gravatar.com bendichter Avatar for h.mayorquin from gravatar.com h.mayorquin Avatar for pauladkisson from gravatar.com pauladkisson

Credits

Author: Cody Baker, Szonja Weigl, Heberto Mayorquin, Luiz Tauffer, and Ben Dichter.

License

BSD-3-Clause

Requires

Python >=3.9

Provides Extra

abf alphaomega audio axona behavior biocam blackrock brukertiff caiman cellexplorer cnmfe compressors csv dandi deeplabcut docs ecephys edf excel extract fictrac full hdf5 icephys intan kilosort lightningpose maxwell mcsraw mearec micromanagertiff miniscope neuralynx neuroscope openephys ophys phy plexon sbx scanimage sima sleap spike2 spikegadgets spikeglx suite2p tdt test text tiff video

Tags

nwb

Classifiers

Report project as malware

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Release history Release notifications | RSS feed

0.10.2

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