pipe.cb

Two-photon + Behavioral Integration - Burgess Lab

pipe.cb has 3 wrappers. Manual input is required after each wrapper:

1. wrapper1: write Tiffs, read+align nidaq, write eye video (.avi) -> Facemap/DLC + jupyter notebook to convert (raise issue)
2. wrapper2: stimuli + behavior -> run Suite2p
3. wrapper3: process neural data from Suite2p, integrate some behavior Begin Spyder analysis

The pipeline is based on inputting entire paths to functions. This avoids common parsing issues, doesn't force folder renames, maintains accurate filePaths, and allows easy portability between machines/servers.

findFILE is integral to running pipe.cb

The only user steps to run pipe.cb are

1. clone this repo
2. clone facemap + Suite2p
3. selecting (indexing) into findFILE to select files for analysis (wrapper1-3)
4. adjusting paths {ijroot (tiffLoop), and bhv file template in bhv2Convert}

To Access Data:

Turbo Instructions

Alexa Faulkner 2020

HUGE THANK YOU TO:

Carsen Stringer, Marius Pachitariu, Arthur Sugden for essential guidance, code and tools!