June 13, 2019
Zach Pennington from Denise Cai’s lab at Mt. Sinai recently posted a preprint describing their latest open-source project called ezTrack:
ezTrack is an open-source, platform independent set of behavior analysis pipelines using interactive Python (iPython/Jupyter Notebook) that researchers with no prior programming experience can use. ezTrack is a sigh of relief for researchers with little to no computer programming experience. Behavioral tracking analysis shouldn’t be limited to those with extensive programming knowledge, and ezTrack is a nice alternative to currently available software that may require a bit more programming experience. The manuscript and Jupyter notebooks are written in the style of a tutorial, and is meant to provide straightforward instructions to the user on implementing ezTrack. ezTrack is unique from other recent video analysis toolboxes in that this method does not use deep learning algorithms and thus does not require training sets for transfer learning.
ezTrack can be used to analyze rodent behavior videos of a single animal in different settings, and the authors provide examples of positional analysis across several tasks (place-preference, water-maze, open-field, elevated plus maze, light-dark boxes, etc), as well as analysis of freezing behavior. ezTrack can provide frame-by-frame data output in .csv files, and users can crop the frames of the video to get rid of any issue with cables from optogenetic or electrophysiology experiments. ezTrack can take on multiple different video formats, such as mpg1, wav, avi, and more.
Aside from the benefit of being open-source, there are several major advantages of ezTrack. Notably, the tool is user-friendly in that it is accessible to researchers with little to no programming background. The user does not need to make many adjustments to parameters of the toolbox, and the data can processed into interactive visualizations and is easily extractable in .csv files. ezTrack is both operating system and hardware independent and can be used across multiple platforms. Utilizing ipython/Jupyter Notebook allows researchers to easily replicate their analyses as well.
Check out their GitHub with more details on how to use ezTrack: https://github.com/denisecailab/ezTrack
Pennington, Z. T., Dong, Z., Bowler, R., Feng, Y., Vetere, L. M., Shuman, T., & Cai, D. J. (2019). ezTrack: An open-source video analysis pipeline for the investigation of animal behavior. BioRxiv, 592592.