Cellular anatomy of the mouse primary motor cortex.

An essential step toward understanding brain function is to establish a structural framework with cellular resolution on which multi-scale datasets spanning molecules, cells, circuits and systems can be integrated and interpreted1. Here, as part of the collaborative Brain Initiative Cell Census Network (BICCN), we derive a comprehensive cell type-based anatomical description of one exemplar brain structure, the mouse primary motor cortex, upper limb area (MOp-ul). Using genetic and viral labelling, barcoded anatomy resolved by sequencing, single-neuron reconstruction, whole-brain imaging and cloud-based neuroinformatics tools, we delineated the MOp-ul in 3D and refined its sublaminar organization. We defined around two dozen projection neuron types in the MOp-ul and derived an input-output wiring diagram, which will facilitate future analyses of motor control circuitry across molecular, cellular and system levels. This work provides a roadmap towards a comprehensive cellular-resolution description of mammalian brain architecture.

Semantic segmentation of microscopic neuroanatomical data by combining topological priors with encoder-decoder deep networks.

Understanding of neuronal circuitry at cellular resolution within the brain has relied on neuron tracing methods which involve careful observation and interpretation by experienced neuroscientists. With recent developments in imaging and digitization, this approach is no longer feasible with the large scale (terabyte to petabyte range) images. Machine learning based techniques, using deep networks, provide an efficient alternative to the problem. However, these methods rely on very large volumes of annotated images for training and have error rates that are too high for scientific data analysis, and thus requires a significant volume of human-in-the-loop proofreading. Here we introduce a hybrid architecture combining prior structure in the form of topological data analysis methods, based on discrete Morse theory, with the best-in-class deep-net architectures for the neuronal connectivity analysis. We show significant performance gains using our hybrid architecture on detection of topological structure (e.g. connectivity of neuronal processes and local intensity maxima on axons corresponding to synaptic swellings) with precision/recall close to 90% compared with human observers. We have adapted our architecture to a high performance pipeline capable of semantic segmentation of light microscopic whole-brain image data into a hierarchy of neuronal compartments. We expect that the hybrid architecture incorporating discrete Morse techniques into deep nets will generalize to other data domains.

A noninvasive swallowing measurement system using a combination of respiratory flow, swallowing sound, and laryngeal motion.

The assessment of swallowing function is important for the prevention of aspiration pneumonia. We developed a new swallowing monitoring system that uses respiratory flow, swallowing sound, and laryngeal motion. We applied this device to 11 healthy volunteers and 10 patients with dysphagia. Videofluoroscopy (VF) was conducted simultaneously with swallowing monitoring using our device. We measured laryngeal rising time (LRT), the time required for the larynx to elevate to the highest position, and laryngeal activation duration (LAD), the duration between the onset of rapid laryngeal elevation and the time when the larynx returned to the lowest position. In addition, we evaluated the coordination between swallowing and breathing. We found that LAD was correlated with a VF-derived parameter, pharyngeal response duration (PRD) in healthy subjects (LAD: 959 ± 259 ms vs. PRD: 1062 ± 149 ms, r = 0.60); however, this correlation was not found in the dysphagia patients. LRT was significantly prolonged in patients (healthy subjects: 320 ± 175 ms vs. PATIENTS: 465 ± 295 ms, P < 0.001, t test). Furthermore, frequency of swallowing immediately after inspiration was significantly increased in patients. Therefore, the new device may facilitate the assessment of some aspects of swallowing dysfunction.