Comprehensive estimates of potential synaptic connections in local circuits of the rodent hippocampal formation by axonal-dendritic overlap

A quantitative description of the hippocampal formation synaptic architecture is essential for understanding the neural mechanisms of episodic memory. Yet the existing knowledge of connectivity statistics between different neuron types in the rodent hippocampus only captures a mere 5% of this circuitry. We present a systematic pipeline to produce first-approximation estimates for most of the missing information. Leveraging the Hippocampome.org knowledge base, we derive local connection parameters between distinct pairs of morphologically identified neuron types based on their axonal-dendritic overlap within every layer and subregion of the hippocampal formation. Specifically, we adapt modern image analysis technology to determine the parcel-specific neurite lengths of every neuron type from representative morphological reconstructions obtained from either sex. We then compute the average number of synapses per neuron pair using relevant anatomical volumes from the mouse brain atlas and ultrastructurally established interaction distances. Hence, we estimate connection probabilities and number of contacts for over 1,900 neuron type pairs, increasing the available quantitative assessments more than 11-fold. Connectivity statistics thus remain unknown for only a minority of potential synapses in the hippocampal formation, including those involving long-range (23%) or perisomatic (6%) connections and neuron types without morphological tracings (7%). The described approach also yields approximate measurements of synaptic distances from the soma along the dendritic and axonal paths, which may affect signal attenuation and delay. Overall, this dataset fills a substantial gap in quantitatively describing hippocampal circuits and provides useful model specifications for biologically realistic neural network simulations, until further direct experimental data become available. SIGNIFICANCE STATEMENT The hippocampal formation is a crucial functional substrate for episodic memory and spatial representation. Characterizing the complex neuron type circuit of this brain region is thus important to understand the cellular mechanisms of learning and navigation. Here we present the first numerical estimates of connection probabilities, numbers of contacts per connected pair, and synaptic distances from the soma along the axonal and dendritic paths, for more than 1,900 distinct neuron type pairs throughout the dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex. This comprehensive dataset, publicly released online at Hippocampome.org, constitutes an unprecedented quantification of the majority of the local synaptic circuit for a prominent mammalian neural system and provides an essential foundation for data-driven, anatomically realistic neural network models.