[Project]: Fiber Photometry Resource Repository

[joshlawrimore]

Title

Fiber Photometry Resource Repository

Leaders

@joshlawrimore

Project Description

• Create a public repository that lists public and open-source data and analysis code for fiber photometry. This repo will serve as a resource scientists and developers to re-use existing code for novel analyses.
• The combination of open-source code and data allows the community to create reproducible analysis pipelines to parse, visualize, and analyze fiber photometry. Creating a community resource repo is the first step to creating standard analysis practices and methods.

Project Goals

• Create a github repository listing and categorizing open source code and data for fiber photometry experiments for Python and MATLAB
• Goal 1: Create the README.MD in the repo is a beginner level task focused on learning git, GitHub, and collaborative coding in a low-code environment. It will cover the basics of local vs remote repository, branching, and merging. It will also cover the basics of using GitHub Issues for task assignment.
• Goal 2: Create example code notebooks that download example data to demonstrate existing open-source tools for parsing, vizualizing, and analyzing fiber photometry data for experienced coders. Allows coders to learn about programmatic data download, Jupyter/Marimo/MATLAB notebook examples, and visualizing data.
• Goal 3: Create a Python or MATLAB package that uses public data to create automatic regression tests with GitHub Actions to ensure code updates do not break existing code. This is an introduction to package creation and testing.

Useful links

Papers with Code

• Fiber Photometry Analysis of Spontaneous Dopamine Signals: The Z-Scored Data Are Not the Data
• FiPhoPHA-A Fiber Photometry Python Package for Post Hoc Analysis
• Optimized workflow for behavior-coupled fiber photometry experiment: improved data navigation and accessibility
• PASTa: An Open-Source Analysis and Signal Processing Toolbox for Fiber Photometry Data
• Obtaining artifact-corrected signals in fiber photometry via isosbestic signals, robust regression, and dF/F calculations
• A statistical framework for analysis of trial-level temporal dynamics in fiber photometry experiments
• FiPhA: an open-source platform for fiber photometry analysis
• PhAT: A Flexible Open-Source GUI-Driven Toolkit for Photometry Analysis
• Integrating operant behavior and fiber photometry with the open-source python library Pyfiber
• GuPPy, a Python toolbox for the analysis of fiber photometry data
• pMAT: An open-source software suite for the analysis of fiber photometry data
   

Source Code Only

• FluoR (R Language)
• FPA (MATLAB)
   

Data

• Dandi Archive

Development status

0_concept_no_content

Type (Select all that apply)

documentation

Modalities (Select all that apply)

other

Programming language (Select all that apply)

Python, Matlab, R

Agreement to Code of Conduct

• I agree to follow BrainHack's Code of Conduct