RT Journal Article SR Electronic T1 COUNTEN, an AI-Driven Tool for Rapid and Objective Structural Analyses of the Enteric Nervous System JF eneuro JO eNeuro FD Society for Neuroscience SP ENEURO.0092-21.2021 DO 10.1523/ENEURO.0092-21.2021 VO 8 IS 4 A1 Kobayashi, Yuta A1 Bukowski, Alicia A1 Das, Subhamoy A1 Espenel, Cedric A1 Gomez-Frittelli, Julieta A1 Wagle, Narayani A1 Bakshi, Shriya A1 Saha, Monalee A1 Kaltschmidt, Julia A. A1 Venkataraman, Archana A1 Kulkarni, Subhash YR 2021 UL http://www.eneuro.org/content/8/4/ENEURO.0092-21.2021.abstract AB The enteric nervous system (ENS) consists of an interconnected meshwork of neurons and glia residing within the wall of the gastrointestinal (GI) tract. While healthy GI function is associated with healthy ENS structure, defined by the normal distribution of neurons within ganglia of the ENS, a comprehensive understanding of normal neuronal distribution and ganglionic organization in the ENS is lacking. Current methodologies for manual enumeration of neurons parse only limited tissue regions and are prone to error, subjective bias, and peer-to-peer discordance. There is accordingly a need for robust, and objective tools that can capture and quantify enteric neurons within multiple ganglia over large areas of tissue. Here, we report on the development of an AI-driven tool, COUNTEN (COUNTing Enteric Neurons), which is capable of accurately identifying and enumerating immunolabeled enteric neurons, and objectively clustering them into ganglia. We tested and found that COUNTEN matches trained humans in its accuracy while taking a fraction of the time to complete the analyses. Finally, we use COUNTEN’s accuracy and speed to identify and cluster thousands of ileal myenteric neurons into hundreds of ganglia to compute metrics that help define the normal structure of the ileal myenteric plexus. To facilitate reproducible, robust, and objective measures of ENS structure across mouse models, experiments, and institutions, COUNTEN is freely and openly available to all researchers.