title: BlastNeuron for Automated Comparison, Retrieval and Clustering of 3D Neuron Morphologies.
abstract: Characterizing the identity and types of neurons in the brain, as well as their associated function, requires a means of quantifying and comparing 3D neuron morphology. Presently, neuron comparison methods are based on statistics from neuronal morphology such as size and number of branches, which are not fully suitable for detecting local similarities and differences in the detailed structure. We developed BlastNeuron to compare neurons in terms of their global appearance, detailed arborization patterns, and topological similarity. BlastNeuron first compares and clusters 3D neuron reconstructions based on global morphology features and moment invariants, independent of their orientations, sizes, level of reconstruction and other variations. Subsequently, BlastNeuron performs local alignment between any pair of retrieved neurons via a tree-topology driven dynamic programming method. A 3D correspondence map can thus be generated at the resolution of single reconstruction nodes. We applied BlastNeuron to three datasets: (1) 10,000+ neuron reconstructions from a public morphology database, (2) 681 newly and manually reconstructed neurons, and (3) neurons reconstructions produced using several independent reconstruction methods. Our approach was able to accurately and efficiently retrieve morphologically and functionally similar neuron structures from large morphology database, identify the local common structures, and find clusters of neurons that share similarities in both morphology and molecular profiles.
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
authors.forename: Yinan
authors.initials: Y
authors.lastname: Wan
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.|Allen Institute for Brain Science, Seattle, WA, USA.
authors.forename: Fuhui
authors.initials: F
authors.lastname: Long
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.|Key Laboratory of Intelligent Computation and Signal Processing, Ministry of Education, Anhui University, Hefei, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Qu
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
authors.forename: Hang
authors.initials: H
authors.lastname: Xiao
authors.affiliation: Allen Institute for Brain Science, Seattle, WA, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Hawrylycz
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.|Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
authors.forename: Eugene W
authors.initials: EW
authors.lastname: Myers
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA. hanchuanp@alleninstitute.org.|Allen Institute for Brain Science, Seattle, WA, USA. hanchuanp@alleninstitute.org.
authors.forename: Hanchuan
authors.initials: H
authors.lastname: Peng
mesh_terms: D000465:Algorithms; D000818:Animals; D001921:Brain / Q000166:cytology; D016000:Cluster Analysis; D003628:Database Management Systems; D006801:Humans; D021621:Imaging, Three-Dimensional; D008959:Models, Neurological; D009474:Neurons / Q000502:physiology*; D017711:Nonlinear Dynamics
keywords: Neuron comparison; Neuron morphology; Neuron reconstruction; Tree matching