For algorithm and backround, see Helmstaedter et al., 2011.
A more recent implementation (used in Hua et al., 2015) can be found here:
Supplementary Software in Hua et al., 2015
1 additional matlab file required for execution:
Skeleton Files (.nml format)
Helmstaedter, M, Briggmann KL, Denk W (2011): High-accuracy neurite reconstruction for high-throughput neuroanatomy. Nature Neuroscience 14:1081-1088 featured in “High-throughput anatomy: Charting the brain's networks.” Nature Neuroscience 490:293–298 PDF
Hua Y, Laserstein P, Helmstaedter, M (2015): Large-volume en-bloc staining for electron microscopy-based connectomics. Nature Communications 6: 7923. PDF