title: SegEM: Efficient Image Analysis for High-Resolution Connectomics.
abstract: Progress in electron microscopy-based high-resolution connectomics is limited by data analysis throughput. Here, we present SegEM, a toolset for efficient semi-automated analysis of large-scale fully stained 3D-EM datasets for the reconstruction of neuronal circuits. By combining skeleton reconstructions of neurons with automated volume segmentations, SegEM allows the reconstruction of neuronal circuits at a work hour consumption rate of about 100-fold less than manual analysis and about 10-fold less than existing segmentation tools. SegEM provides a robust classifier selection procedure for finding the best automated image classifier for different types of nerve tissue. We applied these methods to a volume of 44 × 60 × 141 μm(3) SBEM data from mouse retina and a volume of 93 × 60 × 93 μm(3) from mouse cortex, and performed exemplary synaptic circuit reconstruction. SegEM resolves the tradeoff between synapse detection and semi-automated reconstruction performance in high-resolution connectomics and makes efficient circuit reconstruction in fully-stained EM datasets a ready-to-use technique for neuroscience.
authors.affiliation: Department of Connectomics, Max Planck Institute for Brain Research, Max-von-Laue-Strasse 4, 60438 Frankfurt, Germany. Electronic address: manuel.berning@brain.mpg.de.
authors.forename: Manuel
authors.initials: M
authors.lastname: Berning
authors.affiliation: Department of Connectomics, Max Planck Institute for Brain Research, Max-von-Laue-Strasse 4, 60438 Frankfurt, Germany.
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Boergens
authors.affiliation: Department of Connectomics, Max Planck Institute for Brain Research, Max-von-Laue-Strasse 4, 60438 Frankfurt, Germany. Electronic address: mh@brain.mpg.de.
authors.forename: Moritz
authors.initials: M
authors.lastname: Helmstaedter
mesh_terms: D000818:Animals; D057205:Automation, Laboratory / Q000379:methods*; D063132:Connectome / Q000379:methods*; D006801:Humans; D021621:Imaging, Three-Dimensional / Q000379:methods*; D051379:Mice; D008854:Microscopy, Electron / Q000379:methods*; D012160:Retina / Q000502:physiology / Q000648:ultrastructure*; D014793:Visual Cortex / Q000166:cytology / Q000502:physiology / Q000648:ultrastructure*