MoGen: Detailed Neuronal Morphology Generation via Point Cloud Flow Matching

ICLR 2026 Conference Submission14288 Authors

Keywords: neuroscience, connectomics, neuron reconstruction, generative modelling, point clouds, flow matching

Abstract: Biological neurons come in many shapes. High-fidelity generative modeling of their varied morphologies is challenging yet underexplored in neuroscience, and crucial for the subfield of connectomics. We introduce MoGen (Neuronal Morphology Generation), a flow matching model to generate high-resolution 3D point clouds of mouse cortex axon and dendrite fragments. This is enabled by an adaptation that injects local geometric context into a scalable latent transformer backbone, allowing for the generation of high-fidelity, realistic samples. To assess MoGen's generation quality, we propose a dedicated evaluation suite with interpretable geometric and topological features tailored to neuronal structures that we validate in a user study. MoGen's practical utility is showcased through controllable generation for visualization via smooth interpolation and a direct downstream application: we augment the training set of a shape plausibility classifier from a production connectomics neuron reconstruction pipeline with millions of generated samples, thereby improving classifier accuracy and reducing the number of remaining split and merge errors by 4.4%. We estimate this can reduce manual proofreading labor by over 157 person-years for reconstruction of a full mouse brain.

Primary Area: applications to neuroscience & cognitive science

Submission Number: 14288