NeuronCtrl: Geometry-Aware Safe Closed-Loop Generative Control for Neuronal Microenvironment Dynamics

Neuromodulation can be viewed as closed-loop control of high-dimensional spatiotemporal fields on irregular 3D morphologies, coupling membrane electrophysiology with ionic reaction–diffusion. This view supports high-rate feedback and systematic in-silico evaluation, yet is difficult in practice. Unlike classical PDE control with known equations on regular domains, neuronal microenvironments exhibit complex, often unknown biophysics on irregular shapes. High-fidelity simulators are too costly for real-time control with repeated planning. The discretized field is sparsely observed and must satisfy hard full-field safety constraints. We introduce NeuronCtrl , a modular operator-level framework for safe, closed-loop generative control of neuronal microenvironment dynamics. Given measurements, actions, and morphology, a history-conditioned observer infers the latent field, a morphology-aware neural operator predicts one-step dynamics, and a flow-matching conditional flow proposes actions conditioned on user preferences. Safety is enforced via complementary barrier-based mechanisms at both the action and field levels, ensuring constraint satisfaction with minimal intervention. When latency is critical, the multi-step generator is distilled into a single-step policy while retaining the same safety filter. Experiments across three high-fidelity 3D neuromodulation benchmarks spanning deep brain stimulation, extracellular reaction--diffusion control, and astrocytic potassium regulation, demonstrate superior trade-offs among cost, safety, and latency. Code is available at https://anonymous.4open.science/r/NeuronControl-D900.