The Connectome Interpreter Toolkit

Abstract

Abstract Complete synaptic wiring diagrams, or connectomes, of whole brains open new opportunities for studying the structure-function relationship of neural circuits. However, the large number of nodes and edges in the graphs makes the analysis challenging. Here, we present the Connectome Interpreter , an open-source software toolkit for efficient graph exploration to find polysynaptic pathways, compute the effective connectivity and receptive fields for arbitrarily deep neurons, slice out subcircuits, and construct non-linear but differentiable circuit models, implemented using efficient approaches tailored to large connectomes with abundant divergent and convergent connections, such as that of the fruit fly Drosophila melanogaster . Our approach delivers results orders of magnitude faster than conventional methods on consumer hardware. We demonstrate the capabilities of our toolkit with select applications, including quantifying the density of polysynaptic connections in the whole adult fruit fly brain, exploring the necessity for non-linearities in circuit modeling, and combining known function of neurons with the connectome to aid in formulating hypotheses of circuit function.

Abstract of "The Connectome Interpreter Toolkit" by Yijie Yin, Judith Hoeller, Alexander Mathiasen et al., https://doi.org/10.1101/2025.09.29.679410, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified.