title: Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis.
abstract: Three-dimensional (3D) bioimaging, visualization and data analysis are in strong need of powerful 3D exploration techniques. We develop virtual finger (VF) to generate 3D curves, points and regions-of-interest in the 3D space of a volumetric image with a single finger operation, such as a computer mouse stroke, or click or zoom from the 2D-projection plane of an image as visualized with a computer. VF provides efficient methods for acquisition, visualization and analysis of 3D images for roundworm, fruitfly, dragonfly, mouse, rat and human. Specifically, VF enables instant 3D optical zoom-in imaging, 3D free-form optical microsurgery, and 3D visualization and annotation of terabytes of whole-brain image volumes. VF also leads to orders of magnitude better efficiency of automated 3D reconstruction of neurons and similar biostructures over our previous systems. We use VF to generate from images of 1,107 Drosophila GAL4 lines a projectome of a Drosophila brain.
authors.affiliation: 1] Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA [2] Allen Institute for Brain Science, 551 North 34th Street, Suite 200, Seattle, Washington 98103, USA.
authors.forename: Hanchuan
authors.initials: H
authors.lastname: Peng
authors.affiliation: 1] Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA [2].
authors.forename: Jianyong
authors.initials: J
authors.lastname: Tang
authors.affiliation: 1] Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA [2].
authors.forename: Hang
authors.initials: H
authors.lastname: Xiao
authors.affiliation: 1] Integrated Research Centre, University Campus Bio-Medico of Rome, 00128 Rome, Italy [2] Department of Electrical and Information Engineering, University of Cassino and L.M., 03043 Cassino, Italy [3].
authors.forename: Alessandro
authors.initials: A
authors.lastname: Bria
authors.affiliation: 1] Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA [2].
authors.forename: Jianlong
authors.initials: J
authors.lastname: Zhou
authors.affiliation: Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA.
authors.forename: Victoria
authors.initials: V
authors.lastname: Butler
authors.affiliation: Allen Institute for Brain Science, 551 North 34th Street, Suite 200, Seattle, Washington 98103, USA.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Zhou
authors.affiliation: 1] Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK [2] Program in Sensory Physiology and Behavior, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA.
authors.forename: Paloma T
authors.initials: PT
authors.lastname: Gonzalez-Bellido
authors.affiliation: Allen Institute for Brain Science, 551 North 34th Street, Suite 200, Seattle, Washington 98103, USA.
authors.forename: Seung W
authors.initials: SW
authors.lastname: Oh
authors.affiliation: 1] Department of Pulmonary Medicine, M. D. Anderson Cancer Center, Houston, Texas 77030, USA [2] Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.
authors.forename: Jichao
authors.initials: J
authors.lastname: Chen
authors.affiliation: 1] Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA [2] Circuit Therapeutics, Inc., Menlo Park, California 94025, USA.
authors.forename: Ananya
authors.initials: A
authors.lastname: Mitra
authors.affiliation: 1] Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA [2] New York University Institute of Neuroscience, New York University, New York, New York 10016, USA.
authors.forename: Richard W
authors.initials: RW
authors.lastname: Tsien
authors.affiliation: Allen Institute for Brain Science, 551 North 34th Street, Suite 200, Seattle, Washington 98103, USA.
authors.forename: Hongkui
authors.initials: H
authors.lastname: Zeng
authors.affiliation: Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia 22030, USA.
authors.forename: Giorgio A
authors.initials: GA
authors.lastname: Ascoli
authors.affiliation: Integrated Research Centre, University Campus Bio-Medico of Rome, 00128 Rome, Italy.
authors.forename: Giulio
authors.initials: G
authors.lastname: Iannello
authors.affiliation: Allen Institute for Brain Science, 551 North 34th Street, Suite 200, Seattle, Washington 98103, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Hawrylycz
authors.affiliation: 1] Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA [2] Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
authors.forename: Eugene
authors.initials: E
authors.lastname: Myers
authors.affiliation: 1] Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA [2] Allen Institute for Brain Science, 551 North 34th Street, Suite 200, Seattle, Washington 98103, USA [3] BioImage, L.L.C., Bellevue, Washington 98005, USA.
authors.forename: Fuhui
authors.initials: F
authors.lastname: Long
mesh_terms: D000465:Algorithms; D000818:Animals; D001921:Brain / Q000166:cytology; D017173:Caenorhabditis elegans; D004330:Drosophila; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008168:Lung / Q000166:cytology; D051379:Mice; D008866:Microsurgery / Q000379:methods*; D023421:Models, Animal; D032342:Muscle Cells / Q000166:cytology; D009474:Neurons / Q000166:cytology; D014584:User-Computer Interface