The ENS consists of the submucosal and myenteric plexus (SMP, MP) and controls a variety of gut functions. The quantitative analysis of innervation in the ENS is still a challenge because the ENS forms a mesh-like three-dimensional (3D) network embedded in the gut wall. We developed a computerized approach to perform direct, objective and automatic measurements of innervation in 3D structures of the mouse colonic ENS. The whole mounts of SMP and MP were prepared along the proximal, transverse and distal colon (pC, tC, dC) collected from 8 naïve mice (C57BL/6J, 6 weeks, 4 of each sex). Each 3D image of SMP or MP was reconstructed from Z-stack confocal images with 50-100 or 30-50 optical sections in the frame 1415×1415 or 708×708 μm and 1 μm apart. The Hu C/D, peripheral form of choline acetyltransferase (pChAT), nitric oxide synthase (nNOS), vasoactive intestinal peptide (VIP), tyrosine hydroxylase (TH) and calcitonin gene-related protein (CGRP) immunoreactive (ir) enteric neurons or fibers were digitally traced and automatically measured with Imaris 9.7 for neuroscientists. The co-localization of pChAT and nNOS was determined with ImarisColoc tool. The densities of neurons and nerve fibers, co-localization of pChAT and nNOS were calculated from 6-8 of 3D images/marker/plexus/segment/mouse (total 2304 3D images) and expressed as the percentage of each type of neurons in total neurons, the volume of each type of nerve fibers in the volume of SMP and MP and co-labeled neurons in each type of neurons. The results demonstrate significant differences in the numbers of two major neuronal populations, their co-localization and densities of three representative nerve fibers among three colonic segments, between two plexuses and sexes. 1. pChAT- and nNOS-ir neurons in the MP: the density of pChAT-ir neurons was 1.4- and 2.1-fold lower in the pC than in the tC and dC (p<0.05, p<0.001), and 1.6- and 4.0-fold higher than that of nNOS-ir neurons in the tC and dC (p<0.001, p<0.001), respectively. In contrast, the density of nNOS-ir neurons was 1.4- or 2.3-fold higher in the pC or tC than dC (p<0.001, p<0.01). 2. Co-localization of pChAT and nNOS in the MP: Co-labeled neurons in the nNOS-ir neurons were 1.4- or 1.5-fold lower in the pC or tC than dC (p<0.05, p<0.05). 3. Nerve fibers: The density of VIP-ir fibers in the SMP was 2.4- and 1.8-fold higher in the pC than tC and dC (p<0.001, p<0.001) while 3.0- and 2.4-fold lower than in the MP in both tC and dC (p<0.001, 0.001). TH-ir fibers in the SMP were 1.6-fold lower in both tC or dC than pC (p<0.01, p<0.01), 1.6-, 2.2- and 1.4-fold lower than MP in the pC, tC and dC (p<0.001, p<0.001, p<0.05). In the MP, they were 1.8- and 1.6-fold lower in the dC than in pC and tC (p<0.001, p<0.001). CGRP-ir fibers did not show significant difference between two plexuses among three segments. 4. Sex differences: The co-labeled neurons in the pChAT-ir neurons were 2.2-, 2.7- and 2.2-fold more in the males than females in three segments (p<0.001, p<001, p<0.001) while those in the nNOS-ir neurons were 1.9-fold more in the males than females only in the dC (p<0.05). VIP-ir fibers in the dC-MP were 1.2-fold higher in the males than females (p<0.05). These data and the novel approach developed in this study will contribute to further assessments of the structure-function relationships and pathological alterations in the colon with mouse models. Supported by NIH/SPARC 1OT2OD024899-01. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.