Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis

Hanchuan Peng; Jianyong Tang; Hang Xiao; Alessandro Bria; Jianlong Zhou; Victoria Butler; Zhi Zhou; Paloma T Gonzalez-Bellido; Seung W Oh; Jichao Chen; Ananya Mitra; Richard W Tsien; Hongkui Zeng; Giorgio A Ascoli; Giulio Iannello; Michael Hawrylycz; Eugene Myers; Fuhui Long

doi:10.1038/ncomms5342

Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis

Nat Commun. 2014 Jul 11:5:4342. doi: 10.1038/ncomms5342.

Authors

Hanchuan Peng¹, Jianyong Tang², Hang Xiao², Alessandro Bria³, Jianlong Zhou², Victoria Butler⁴, Zhi Zhou⁵, Paloma T Gonzalez-Bellido⁶, Seung W Oh⁵, Jichao Chen⁷, Ananya Mitra⁸, Richard W Tsien⁹, Hongkui Zeng⁵, Giorgio A Ascoli¹⁰, Giulio Iannello¹¹, Michael Hawrylycz⁵, Eugene Myers¹², Fuhui Long¹³

Affiliations

¹ 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.
² 1] Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA [2].
³ 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].
⁴ Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA.
⁵ Allen Institute for Brain Science, 551 North 34th Street, Suite 200, Seattle, Washington 98103, USA.
⁶ 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.
⁷ 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.
⁸ 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.
⁹ 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.
¹⁰ Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia 22030, USA.
¹¹ Integrated Research Centre, University Campus Bio-Medico of Rome, 00128 Rome, Italy.
¹² 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.
¹³ 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.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Animals
Brain / cytology
Caenorhabditis elegans
Drosophila
Image Processing, Computer-Assisted / methods*
Imaging, Three-Dimensional / methods*
Lung / cytology
Mice
Microsurgery / methods*
Models, Animal
Muscle Cells / cytology
Neurons / cytology
User-Computer Interface*

Abstract

Publication types

MeSH terms

Grants and funding