Real-time, low-latency closed-loop feedback using markerless posture tracking

The ability to control a behavioral task or stimulate neural activity based on animal behavior in real-time is an important tool for experimental neuroscientists. Ideally, such tools are noninvasive, low-latency, and provide interfaces to trigger external hardware based on posture. Recent advances in pose estimation with deep learning allows researchers to train deep neural networks to accurately quantify a wide variety of animal behaviors. Here, we provide a new DeepLabCut-Live! package that achieves low-latency real-time pose estimation (within 15 ms, >100 FPS), with an additional forward-prediction module that achieves zero-latency feedback, and a dynamic-cropping mode that allows for higher inference speeds. We also provide three options for using this tool with ease: (1) a stand-alone GUI (called DLC-Live! GUI), and integration into (2) Bonsai, and (3) AutoPilot. Lastly, we benchmarked performance on a wide range of systems so that experimentalists can easily decide what hardware is required for their needs.

Mapping the human subcortical auditory system using histology, postmortem MRI and in vivo MRI at 7T

Studying the human subcortical auditory system non-invasively is challenging due to its small, densely packed structures deep within the brain. Additionally, the elaborate three-dimensional (3-D) structure of the system can be difficult to understand based on currently available 2-D schematics and animal models. Wfe addressed these issues using a combination of histological data, post mortem magnetic resonance imaging (MRI), and in vivo MRI at 7 Tesla. We created anatomical atlases based on state-of-the-art human histology (BigBrain) and postmortem MRI (50 µm). We measured functional MRI (fMRI) responses to natural sounds and demonstrate that the functional localization of subcortical structures is reliable within individual participants who were scanned in two different experiments. Further, a group functional atlas derived from the functional data locates these structures with a median distance below 2 mm. Using diffusion MRI tractography, we revealed structural connectivity maps of the human subcortical auditory pathway both in vivo (1050 µm isotropic resolution) and post mortem (200 µm isotropic resolution). This work captures current MRI capabilities for investigating the human subcortical auditory system, describes challenges that remain, and contributes novel, openly available data, atlases, and tools for researching the human auditory system.