Behaviour

Collection of shared utilities to process and analyse behaviour data

Installation

Install with

pip install git+https://github.com/BrancoLab/Behaviour.git

Update with:

pip install git+https://github.com/BrancoLab/Behaviour.git --upgrade

The function in this repository require fc utils, please install/upgrade it with:

pip install git+https://github.com/FedeClaudi/fcutils.git --upgrade

USAGE

TDMS

Collection of functions useful for handling .tdms files from mantis.

utils.py

Functions to open, parse and save .tdms files

mantis_videoframes_test.py

Functions to check if frames where dropped in a mantis recording (using video and metadata files).

TRACKING

Functions for post processing and handling of DLC output

roi_stats.py

Code to use DLC tracking to check time spent in user defined ROIs

tracking.py

Post processing of DLC tracking data: median filtering, computation of kinematics, body-segments analysis etc

SIGNALS [utilities > signals.py]

Code to analyse 1d time series to extract relevant events (e.g. stimuli onsets from a LDR trace)

VIDEOS

utils.py

Lot's of useful stuff for handling, loading and saving videos with opencv.

trial_videos.py

Code to create a video with short clips for each trial within an experimental session