Ctrax extensions for tracking in difficult lighting conditions

TL;DR

This paper presents extensions to the Ctrax fly tracking software that improve tracking accuracy in challenging lighting conditions, such as shadows and lighting changes, which are increasingly relevant with new optogenetic tools.

Contribution

The authors developed and demonstrated Ctrax extensions that enable accurate tracking under difficult lighting conditions, including shadow handling and lighting change adaptation.

Findings

Effective tracking in shadowed environments

Handling of lighting on/off transitions

Extensions applicable to various challenging lighting scenarios

Abstract

The fly tracking software Ctrax by Branson et al. is popular for positional tracking of animals both within and beyond the fly community. Ctrax was not designed to handle tracking in difficult lighting conditions with strong shadows or recurring "on"/"off" changes in lighting - a condition that will likely become increasingly common due to the advent of red-shifted channelrhodopsin. We describe Ctrax extensions we developed that address this problem. The extensions enabled good tracking accuracy in three types of difficult lighting conditions in our lab. Our technique handling shadows relies on "single animal tracking"; the other techniques should be widely applicable.