Tilbury, R. | bioRxiv Science

bioRxiv2026

Spatially resolved transcriptomic identification of thousands of neurons recorded in vivo.

Transcriptomics has transformed our understanding of the brain, but assigning transcriptomic identities to neurons recorded in vivo remains challenging at scale. Existing platforms can pair transcriptomic identity with two-photon calcium imaging in small populations of approximately 100 neurons, but they require recorded cells to be sparse and therefore cannot be applied to large population recordings. Here, we present coppaFISH 3D, a spatially resolved transcriptomics method, and CASTalign, an in silico alignment framework, which together enable transcriptomic identification of thousands of simultaneously recorded cells. coppaFISH 3D detects hundreds of genes in thick 50m fixed sections while preserving tissue integrity, enabling both 3D registration to in vivo imaging and integration with immunofluorescence labelling. The platform is fully powered by open chemistry and open source software, runs on commodity hardware, and can be performed at very low cost per section. It therefore enables transcriptomic identification of recorded neurons at scale, making it possible to study how transcriptomic identity shapes activity in neural populations.

neuroscience↗

bioRxiv2025

Characterizing neuronal population geometry with AI equation discovery

The activity of visual cortical neurons forms a population code representing image stimuli. There is, however, a discrepancy between our understanding of this code at the single-cell and population levels: direct measurements indicate the population code is high-dimensional, but established models of single-cell tuning give rise to low-dimensional codes. We reconciled this discrepancy by developing an AI science system to find a new parsimonious, interpretable equation for visual cortical orientation tuning. Candidate equations were expressed as short computer programs and evolved by Large Language Models (LLMs) using graphical diagnostics. The resulting equation not only improved single-cell fits, but also accurately modelled the population codes high-dimensional geometry. A novel parameter of the AI-discovered equation, which controls single-cell tuning smoothness, gives rise to high-dimensional population codes. The same parameter drives high-dimensional coding in head-direction cells, suggesting a common coding strategy across brain regions. We used this equation to hypothesize a circuit mechanism generating high-dimensional population codes, and to demonstrate the advantages of these codes in a simulated hyperacuity task. These results show that tuning smoothness has a key role in controlling population code geometry, and demonstrate how AI equation discovery can deliver interpretable models accelerating scientific understanding in neuroscience and beyond.

neuroscience↗