NeuroDAP

NeuroDAP (Neuroscience Data Analysis Pipeline) is a MATLAB based pipeline for recording, synchronization, preprocessing, and analysis of neuropixel, photometry, camera, and behavior recordings.

It is developed by Shun Li in Bernardo Sabatini lab, Harvard Medical School.

General structure

NeuroDAP are built with four major stages in mind with variable levels of customization.

1. Recording phase: customize based on rig configuration, such as defining sync pulse is stored in channel 1, licking in channel 2, GCaMP in channel 3 etc
2. Preprocessing phase: synchronize between acquisition systems through common sync pulse, assign a common timestamp to every sample of each recording system
3. Session analysis: extract trial table for each session; align signals and perform basic analysis of these aligned signals; plot session summary
4. Experiment analysis: pooled all sessions across all animals; perform data analysis

Please refer to the wiki section for more detail documentation in the Wiki.

Introduction of sample data set

The sample data set is recorded by Shun Li in 2023. It contains two parts: 1）a sample recording session for showing preprocessing/session analysis phase 2）a sample animals struct for showing experiment analysis phase. The animals struct contains 4 animals, with 1 animals with off-target expression ('SL137'). dLight signals in NAc, pupil/Eye area, and lick are simultaneously recorded for all sessions.

There are 5 major phases:

1. Random: water, airpuff, EP stim, and tone (75dB) are delivered randomly
2. Reward1/2: where EP stim and tone are paired with water
3. Punish1/2: where EP stim and tone are paired with airpuff
4. Timeline: Random (2 sessions) -> Reward1 (3 sessions) -> Punish1 (3 sessions) -> Reward2 (3 sessions) -> 1 week rest -> Punish2 (3 sessions but 3 animals)

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