guppy-neuro

Pre-release

This release is a pre-release and may not be stable for production use.

Guided Photometry Analysis in Python, a free and open-source fiber photometry data analysis tool.

GuPPy 2.0 is in beta. pip install guppy-neuro installs a pre-release. If you need a stable version, see Older versions.

Quick start

Requires Python 3.10 or greater. We recommend installing into a conda environment:

conda create -n guppy_env python=3.12
conda activate guppy_env
pip install guppy-neuro

Then launch the user interface:

guppy

See the installation guide for the full walkthrough, including installing conda and installing from source.

Documentation

The GuPPy documentation lives at guppy.readthedocs.io: a tutorial walking through a first analysis end to end, how-to guides for individual tasks, explanations of how the analysis works, and a reference for every input parameter and output file.

Citation

If you use GuPPy for your research, please cite Venus N. Sherathiya, Michael D. Schaid, Jillian L. Seiler, Gabriela C. Lopez, and Talia N. Lerner GuPPy, a Python toolbox for the analysis of fiber photometry data

Venus N. Sherathiya, Michael D. Schaid, Jillian L. Seiler, Gabriela C. Lopez, and Talia N. Lerner GuPPy, a Python toolbox for the analysis of fiber photometry data. Sci Rep 11, 24212 (2021). https://doi.org/10.1038/s41598-021-03626-9

Contributors

Older versions

No GuPPy 2.0 stable release has been published yet. If you need a stable version, use GuPPy v1.3.0. It predates the 2.0 rewrite and is not installable with pip: download the source from that release, then from inside the unpacked folder run

# Substitute spec_file_windows10.txt or spec_file_linux.txt for your OS.
conda create --name guppy --file spec_file_mac.txt
conda activate guppy
panel serve --show GuPPy/savingInputParameters.ipynb

v1.3.0 has a different interface and different parameters, so the documentation at guppy.readthedocs.io does not apply to it. Use the GitHub Wiki instead.

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