DySTrack: a modular smart microscopy tool for live tracking of dynamic samples on modern commercial microscopes

Abstract

Advances in microscopy and bioimage analysis are enabling unprecedented quantitative observation of dynamic biological systems. Smart microscopy closes the loop by feeding back image-derived information to control image acquisition on the fly, paving the way for increasingly autonomous and sophisticated experiments. However, adoption of smart microscopy remains limited primarily to specialists, and even simple tasks such as live tracking of moving samples are still widely handled manually. Here we describe DySTrack, a modular open-source python tool that serves as a minimal bridge between commercial acquisition software and arbitrary image analysis pipelines, allowing users to stick with familiar vendor-developed user interfaces for microscope configuration whilst leveraging the powerful and platform-agnostic python ecosystem for image analysis. DySTrack comes with detailed documentation and with ready-to-use, easy-to-adapt example pipelines that track moving tissues (namely the zebrafish lateral line primordium and the chick Hensens node) during embryonic development. We hope DySTrack will contribute to a recent push to make smart microscopy more widely accessible.