pMAT: An Open-Source, Modular Software Suite for the Analysis of Fiber Photometry Calcium Imaging

Abstract

The combined development of new technologies for neuronal recordings and the development of novel sensors for recording both cellular activity and neurotransmitter binding has ushered in a new era for the field of neuroscience. Among these new technologies is fiber photometry, a technique wherein an implanted fiber optic is used to record signals from genetically encoded fluorescent sensors in bulk tissue. Fiber photometry has been widely adapted due to its cost-effectiveness, ability to examine the activity of neurons with specific anatomical or genetic identities, and the ability to use these highly modular systems to record from one or more sensors or brain sites in both superficial and deep-brain structures. Despite these many benefits, one major hurdle for laboratories adopting this technique is the steep learning curve associated with the analysis of fiber photometry data. This has been further complicated by a lack of standardization in analysis pipelines. In the present communication, we present pMAT, a ‘photometry modular analysis tool’ that allows users to accomplish common analysis routines through the use of a graphical user interface. This tool can be deployed in MATLAB and edited by more advanced users, but is also available as an independently deployable, open-source application.

Neural circuitry for maternal oxytocin release induced by infant cries

“…Data from both the 470 (signal) and 405 (control) wavelength channels were independently filtered using a sliding window (Bruno et al, 2020). The scale of the control channel was normalized using a least-squares regression of the 470 and 405 wavelength channels.…”

GuPPy, a Python toolbox for the analysis of fiber photometry data

“…We were motivated to develop GuPPy to standardize our own lab's analyses, to allow new users to engage quickly with the technology, and to enable sharing across the community of FP users to avoid unnecessary duplications of effort. Currently, only one other FP analysis tool, pMAT 10 , is publicly available. While valuable, this tool is programmed in MATLAB, a platform that requires a paid subscription to use, and works only with a Windows operating system.…”

“…In the existing literature using FP, data analysis between groups has varied and has mostly been reported as "custom analysis." To date, only one published analysis tool box exists 10 . Although very effective, this tool limits users to MATLAB software run on the Windows operating system.…”

Optogenetic activation of the ventral tegmental area-hippocampal pathway facilitates rapid adaptation to changes in spatial goals

“…Fiber photometry data were recorded using TeleFipho software (BioResearch Center, Co., Ltd., Japan) at a sampling rate of 100 Hz to capture both raw photometry data and event data for optogenetic stimuli. These data were analyzed using pMAT 32 to obtain the % ΔR/R 0 and Z-scores of the peri-event time histograms across the 180 experimental sessions. The time window for this analysis was 1s before and 8s after the start of the stimulation, with a baseline sampling window of 1s immediately before the start of the stimulation and a bin constant of 0.1s.…”