A medial entorhinal connectome reveals compartmentalized microcircuit architecture

The medial entorhinal cortex (MEC) transforms multimodal inputs into spatial representations, but the synaptic architecture underlying its computations remains unclear. Here we generated a synapse-resolution connectomic dataset spanning all six layers of mouse MEC and the adjacent parasubiculum with serial electron microscopy, providing a continuous volume for mapping cellular organization and connectivity across layers and regions. We found that clustered pyramidal neurons in MEC layer II extended oblique apical dendrites with a dorsolateral bias and long-range myelinated axons within the layer. Exhaustive reconstruction of one cluster revealed a central exclusion core (ExC) that spatially partitioned basal dendritic architecture and synaptic connectivity. A spatially constrained growth model reproduced the position-dependent dendritic patterns. Within the ExC, pyramidal neurons formed a compact recurrent excitatory network and converged onto shared inhibitory partners. Basket cells (BC) and recurrent Martinotti cells provided perisomatic and apical-dendritic feedback, respectively. Dense, compact reciprocal connectivity between L2P neurons and BCs within the ExC, together with BC axonal bands extending beyond the ExC, suggests a potential circuit mechanism for generating temporally structured inhibitory output from the pyramidal-cell cluster along directionally extended axons. Together, these findings link cellular-scale geometry and synaptic wiring to emergent circuit dynamics that extend from dense computation within individual clusters to region-wide modulation, providing a connectomic foundation for understanding the circuit basis of spatial navigation.