FiPhA (Fiber Photometry Analysis) is a platform for interactive dataset exploration, event visualization, and summary analysis of fiber photometry datasets in neurobehavior experiments.
Alongside a variety of data transformations, event series can be defined as sets of named intervals of interest relative to a given event signal, with filters that allow for their refinement and a variety of normalizations for standardizing individual responses. The resulting event datasets can be analyzed using the built-in statistical tools or exported for further processing in other applications.
Visualizations use the plotly library, have a number of configurable display options and can be saved at the click of a button. Entire sessions can be saved for later retrieval, and all datasets used during processing exist as data.table/data.frame objects in a central R object for future reference even without the application.
Installation
FiPhA was developed using R v4.2.x and RStudio v2023.x.
You can install the latest development branch as a package directly from GitHub using the devtools package in RStudio with the following commands:
# install devtools if not already (or `remotes`)
install.packages("devtools")
# download and install FiPhA package branch from github
devtools::install_github("mfbridge/FiPhA@pkg")Getting Started
Once installed, FiPhA can be started by navigating to its entry within the RStudio Addins menu. Alternatively, it can be started directly from the console by entering FiPhA::FiPhA().
User Guide
See the user guide for more complete details and examples.
Acknowledgements
This work was supported by the National Institute of Environmental Health Sciences under contract GS-00F-173CA-75N96021F00109 to Social and Scientific Systems, a DLH Holdings Corp. Company.
License
See here.