OVERVIEW

Towards Programmable Neuroscience: Functional Single Cell Omics is organized by Neuroscience School of Advanced Studies (NSAS) and will be held from May 23 - 30, 2026 in Venice, Veneto, Italy.

Description:
The rapid expansion of single-cell omics, dynamic imaging, and optogenetics now provides an unprecedented opportunity not only to analyse cells but also to reverse-engineer and program cell biology at subcellular resolution. This Advanced Course builds on two decades of single-cell and subcellular omics tools to propose the next generation of neuroscience—closing the loop between experimental investigation, AI analysis and understanding.

Over the past twenty years, single-cell omics has revolutionized neuroscience by revealing the vast cellular diversity and dynamic states underlying brain function. Integrating advanced optical imaging has been central to this transformation, adding spatial and temporal context that bulk approaches ignored and even single-cell transcriptomic, epigenomic, and proteomic studies could not fully capture. Molecular profiling, combined with high-resolution imaging, reveals the spatial organization and functional architecture of neural circuits. Imaging informed by omics enables us to observe neuronal differentiation, synaptic wiring, and circuit maturation in real-time, situating molecular data within an anatomical and physiological context. New technologies—including spatial transcriptomics, in situ chromatin mapping, proximity labelling, mass spectrometry, and live-cell super-resolution microscopy—have uncovered how microenvironments shape cell identity, how astrocytes and microglia form specialised niches, and how neurons remodel synapses during learning.

Optical tools, however, do more than observe—they manipulate. Light-based methods can control transfection, gene expression, and cell physiology, expanding the scope of experimental approaches and enabling AI-guided discovery. Photocontrol provides the spatial and temporal precision required for both “AI in the loop” (rich, high-dimensional data analysis and perturbation testing) and “lab in the loop” (AI-guided experimental design focused on the most informative readouts). Together, these approaches accelerate the cycle of data collection, analysis, and discovery.

This convergence has transformed our understanding of neural disease. Single-cell omics can identify pathogenic cell states, such as dopaminergic neurons in Parkinson’s disease, hyperexcitable glutamatergic neurons in epilepsy, or reactive microglia in Alzheimer’s disease. At the same time, imaging places them within disrupted circuits. Advanced imaging tracks synaptic loss, glial activation, and organelle trafficking defects, directly linking molecular abnormalities to circuit dysfunction. These insights are reshaping therapy: imaging-guided single-cell profiling enables precise targeting of disease-driving cell types with gene or RNA therapies, neuroprotective compounds, or glial modulators. Imaging biomarkers of neural activity, connectivity, and organelle dynamics complement molecular biomarkers from CSF and blood, advancing early diagnosis and treatment monitoring. Collectively, the integration of single-cell omics, high-resolution imaging, and AI analysis marks a paradigm shift: moving from static, averaged views of the brain to dynamic, spatially resolved maps of cellular identity and function. This framework not only deepens our understanding of neural circuits but also lays the groundwork for personalised therapies. With these tools, biology-informed functional modelling becomes possible, enabling informed experimental manipulation of cell function.

The Advanced Course will provide a foundation for critically evaluating the interface between single-cell omics, imaging and neuronal function. Through lectures, paper discussions, and guided analyses, participants will focus on framing scientific questions, weighing the strengths and limitations of each approach, and interpreting data to uncover mechanisms of cellular function.