Decoding brain anatomy from neuronal neighborhoods with MYCEL

Abstract Extracellular recordings carry information about neuronal location, and pooling per-unit predictions across neighboring electrodes improves its readout, but whether this local pooling should be learned is untested. We present MYCEL (Message-passing Yields Cellular Embeddings of Location), a graph neural network whose nodes are spike-sorted units carrying waveform and spike-timing features selected on cell-type ground truth, and whose edges encode recording geometry. On the Allen Brain Observatory Visual Coding Neuropixels dataset, learned message passing outperforms fixed aggregation, with the largest gains where single units are least informative. On the International Brain Laboratory Brain Wide Map, MYCEL matches the strongest population model at one-tenth the pairwise interactions. On held-out animals, the embeddings recover laminar depth within visual cortex. Retrained with only the edge geometry changed, the same framework decodes anatomy in macaque visual cortex and human medial temporal lobe. Thus, how neighboring neurons are combined matters as much as the features that describe them.