For analysis of fiber photometry recordings and alignment with SimBA output in MATLAB
Written for photometry data recorded with Neurophotometrics FP3001 system. Experiment details here: https://www.biorxiv.org/content/10.1101/2022.03.28.486055v1 additional packages are needed to run initial photometry processing code. Details in FearLearning3ROIregression_GCaMP. Behavior videos were tracked post-hoc using DeepLabCut https://github.com/DeepLabCut/DeepLabCut Freezing behavior was auto-scored using SimBA https://github.com/sgoldenlab/simba
Analysis pipeline is as follows:
- photometry data initially processed using FearLearning3ROIregression_GCaMP, which writes out an excel file with processed, z-scored data for each mouse.
- Spikes were detected in cell body recordings using SpikeThresholding_GCaMP.
- Start and end time of each freezing bout was determined using DetectBouts
- Spikes and behavior data were aligned using SpikesDuringFreezing_GCaMP. For GCaMP terminal recordings, the average z-score during each bout of freezing and mobility was calculated using AVGZDuringFreezingEpoch_GCaMP