guppy-neuro 2.0.0b4

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

• Venus Sherathiya
• Michael Schaid
• Jillian Seiler
• Gabriela Lopez
• Talia Lerner
• Paul Adkisson-Floro

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.