PointTree: Automatic and accurate reconstruction of long-range axonal projections of single-neuron

Single-neuron axonal projections reveal the route map of neuron output and provide a key cue for understanding how information flows across the brain. Reconstruction of single-neuron axonal projections requires intensive manual operations in tens of terabytes of brain imaging data, and is highly time-consuming and labor-intensive. The main issue lies in the need for precise reconstruction algorithms to avoid reconstruction errors, yet current methods struggle with densely distributed axons, focusing mainly on skeleton extraction. To overcome this, we introduce a point assignment-based method that uses cylindrical point sets to accurately represent axons and a minimal information flow tree model to suppress the snowball effect of reconstruction errors. Our method successfully reconstructs single-neuron axonal projections across hundreds of GBs images with an average of 80% F1-score, while current methods only provide less than 40% F1-score reconstructions from a few hundred MBs images. This huge improvement is helpful for high-throughput mapping of neuron projections.