An autonomous robotic system for high-throughput phenotyping and behavioral studies of individual fruit flies

The fruit fly, Drosophila melanogaster, is a widely used model species in biomedical research. Despite its importance, conducting manual experiments with individual fruit flies can be challenging and time-consuming, especially for studies of individual fly behaviors. Such studies often involve cumbersome preparatory steps, such as manually tethering a fly and then positioning it within an experimental setup1,2. These procedures commonly require the fly to be anesthetized, and, before behavioral assessments begin, the fly must recover from anesthesia. Hence, the introduction of automated phenotyping and behavioral assays would expedite important aspects of fly research, by minimizing manual handling of flies and decreasing the net time needed for experiments. Here, we introduce FlyMAX (Fly Manipulation and Autonomous eXperimentation), an autonomous robotic system for manipulating adult flies without use of anesthesia. FlyMAX collects individual flies from a standard vial, analyzes them with computer vision, and achieves a throughput of >1,000 flies per day for high-throughput inspection and characterization assays. Robotic handling had no detectable adverse effects on fly longevity or our assessments of fly health. Moreover, the behavioral performance of flies, especially of males, was better and less variable than of flies handled manually. Our system employs deep learning-based machine vision for real-time assessments of picking quality and fly phenotypes. This enables fully pipelined, autonomous experimentation for behavioral assays with individual flies in controlled environments, which was previously infeasible. Overall, FlyMAX constitutes a promising technology to enhance the efficiency and reproducibility of research with flies and other insects in fields such as genetics, neuroscience, and drug screening.