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Add SyNCoPy to Tools page #158

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rly opened this issue May 29, 2024 · 2 comments
Open

Add SyNCoPy to Tools page #158

rly opened this issue May 29, 2024 · 2 comments
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tools proposals to add NWB-related tools to glossary

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@rly
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rly commented May 29, 2024

SyNCoPy is a Python package for the analysis of large-scale electrophysiological data. It is similar to the well-established FieldTrip framework, which is an open-source Matlab toolbox for advanced analysis of electrophysiological data.

Preprint: https://www.biorxiv.org/content/10.1101/2024.04.15.589590v1

From a feature perspective, SyNCoPy currently focuses on preprocessing of raw data, time frequency analysis and connectivity measures. We expect that neuroscience users may want to employ SyNCoPy in combination with other well-established software packages like MNE Python, Elephant (Denker et al., 2023) and others that contain complementary functionality. To facilitate this, we provide support for converting MNE Python data structures and importing and exporting standard file formats like NWB. Also, the SyNCoPy file format is based on the open standards HDF5 and JSON, and can thus be read by standard libraries available for a variety of languages.

Docs: https://syncopy.readthedocs.io/en/latest/
Docs about import from and export to NWB: https://syncopy.readthedocs.io/en/latest/user/data_basics.html#data-basics

Source code: https://github.com/esi-neuroscience/syncopy
Export NWB: https://github.com/esi-neuroscience/syncopy/blob/master/syncopy/io/nwb.py
Read NWB: https://github.com/esi-neuroscience/syncopy/blob/master/syncopy/io/load_nwb.py
(I haven't inspected their NWB code)

Logo: https://raw.githubusercontent.com/esi-neuroscience/syncopy/master/doc/source/_static/syncopy_logo_small.png

@rly
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rly commented May 29, 2024

Hi @tensionhead, the NWB team would like to add SyNCoPy to our catalog of community analysis and visualization tools that support the NWB data standard: https://nwb-overview.readthedocs.io/en/latest/tools/analysis_tools_home.html#extracellular-electrophysiology-tools

Could you provide 1-3 sentences describing SyNCoPy for us to put on the catalog? You can see the catalog link above for examples. We would also add the logo and links to the Docs, Source Code, and Preprint. Let us know if there is anything else you would like us to include. Thank you!

@tensionhead
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Hi @rly thanks for reaching out! Great that you want to add our syncopy package to your catalogue 🚀
Happy to provide a few sentences:

SyNCoPy is a Python library providing high level functions for electrophysiological time series and spike data analysis. It allows to conveniently perform complex analysis workflows including data preprocessing, time-frequency and connectivity analysis. SyNCoPy is specifically tailored for very large ("bigger than memory") datasets, leveraging parallelized computation on many different platforms. It is designed after the well established FieldTrip MatLab package and supports MNE Python, NWB and FieldTrip data formats.

Let me know if you need anything else, thx!

@stephprince stephprince added the tools proposals to add NWB-related tools to glossary label Nov 21, 2024
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