FibPho: Analysis Protocol

Each animal has one folder per recording session generated by Synapse with all the fiber photometry recording data from that session. Make a copy of the

trialData.mat 
``` generated by the behavior code from that same session and add it to the folder.

To analyze the fiber photometry signals time-locked to the behavioral trials, across multiple behavior sessions for one animal, run the MATLAB code

fibpho_averaging_acrossdays(Cohort, Mouse, Bank)

• This saves a

Cohort_Mouse_allTrials_fibdat_dFF.mat
``` variable with the raw 415nm and 465nm signals and the calculated dF/F signal per behavior trial

Copy the

Cohort_Mouse_allTrials_fibdat_dFF.mat
``` variables from all mice in an experimental condition into one folder

Run the MATLAB code

fibpho_averaging_acrossMice
``` to combine and analyze trial-based fiber photometry signals across animals.

Modify the

“ExperimentalStage” 
```variable (line 39) to generate the data for the specific session/trials you are interested in.

This code calculates a mean dF/F signal per animal for the cue and reward time windows, and prints them to the command line.

This code also generates the across time waveform plots for visualization of mean and SEM, as in Figure 3 and Ext. Figure 4.

Use the MATLAB code

BootFitDifferencePlot
``` to analyze the difference between groups and generate Ext. Fig 4b.

X values = cue-burst sessions 6-10 (

ExperimentalStage = ‘XCRIT’
```).

Y values = reward-omission pause first 4 extinction trials (

ExperimentalStage = ‘B1’
```).

Exclude mice with recording signals too low to detect pauses (X < 1).

Use the MATLAB code

TwoGroupsMeanDiff
``` with the mean dF/F values of the included mice (calculated above) to generate the Gardner-Altman plots in Figure 3 and Ext. Figure 4