title: A multiscale parallel computing architecture for automated segmentation of the brain connectome.
abstract: Several groups in neurobiology have embarked into deciphering the brain circuitry using large-scale imaging of a mouse brain and manual tracing of the connections between neurons. Creating a graph of the brain circuitry, also called a connectome, could have a huge impact on the understanding of neurodegenerative diseases such as Alzheimer's disease. Although considerably smaller than a human brain, a mouse brain already exhibits one billion connections and manually tracing the connectome of a mouse brain can only be achieved partially. This paper proposes to scale up the tracing by using automated image segmentation and a parallel computing approach designed for domain experts. We explain the design decisions behind our parallel approach and we present our results for the segmentation of the vasculature and the cell nuclei, which have been obtained without any manual intervention.
authors.affiliation: Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA. sylvain@csail.mit.edu
authors.forename: Sylvain
authors.initials: S
authors.lastname: Jaume
authors.forename: Kathleen
authors.initials: K
authors.lastname: Knobe
authors.forename: Ryan R
authors.initials: RR
authors.lastname: Newton
authors.forename: Frank
authors.initials: F
authors.lastname: Schlimbach
authors.forename: Melanie
authors.initials: M
authors.lastname: Blower
authors.forename: R Clay
authors.initials: RC
authors.lastname: Reid
mesh_terms: D000818:Animals; D003198:Computer Simulation; D007090:Image Interpretation, Computer-Assisted / Q000379:methods; D021621:Imaging, Three-Dimensional / Q000379:methods; D051379:Mice; D008854:Microscopy, Electron / Q000379:methods*; D008953:Models, Anatomic; D008959:Models, Neurological; D009415:Nerve Net / Q000648:ultrastructure*; D009474:Neurons; D010363:Pattern Recognition, Automated / Q000379:methods*; D013569:Synapses / Q000648:ultrastructure*; D014793:Visual Cortex / Q000648:ultrastructure*