Neuron Segmentation

Dense neuron segmentation in EM is an instance segmentation task. The canonical pipeline first predicts an affinity map (the connectivity of each voxel to its neighbors) with an encoder-decoder, then converts the affinity map into a segmentation via watershed or a similar algorithm. Evaluation uses the Rand Index and Variation of Information.

This section covers two benchmarks:

• SNEMI3D — the classic small isotropic-anisotropic benchmark, used for end-to-end affinity training and waterz post-processing.

• NISB / BANIS — a larger, anisotropic benchmark with reproduction targets in tutorials/neuron_nisb/.

• SNEMI3D
• NISB / BANIS