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

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

Research output: Contribution to journal › Article › peer-review

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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.

Original language	English (US)
Article number	4342
Journal	Nature communications
Volume	5
DOIs	https://doi.org/10.1038/ncomms5342
State	Published - Jul 11 2014
Externally published	Yes

Bibliographical note

Funding Information:
We thank Z. Ruan and Y. Zhuang for tracing neuritis; T. Lee, G. Rubin and J. Simpson for providing fruit fly neuron images; J. Simpson and P. Chung for providing fruit fly brain slides; R. Kerr for discussion of the imaging and sample preparation methods; C. Doe for providing Drosophila last embryo images; X. Liu and S. Kim for providing some of the C. elegans samples; P. Kochunov for providing human angiographies from magnetic resonance imaging; and S. Ball for proofreading of the manuscript. This work was mainly supported by Howard Hughes Medical Institute. H.P. is currently supported by the Allen Institute for Brain Science. R.W.T. and A.M. were supported by a grant MH071739 (MERIT).

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Peng, H., Tang, J., Xiao, H., Bria, A., Zhou, J., Butler, V., Zhou, Z., Gonzalez-Bellido, P. T., Oh, S. W., Chen, J., Mitra, A., Tsien, R. W., Zeng, H., Ascoli, G. A., Iannello, G., Hawrylycz, M., Myers, E., & Long, F. (2014). Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis. Nature communications, 5, Article 4342. https://doi.org/10.1038/ncomms5342

Peng, H, Tang, J, Xiao, H, Bria, A, Zhou, J, Butler, V, Zhou, Z, Gonzalez-Bellido, PT, Oh, SW, Chen, J, Mitra, A, Tsien, RW, Zeng, H, Ascoli, GA, Iannello, G, Hawrylycz, M, Myers, E & Long, F 2014, 'Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis', Nature communications, vol. 5, 4342. https://doi.org/10.1038/ncomms5342

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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.",

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

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AU - Peng, Hanchuan

AU - Tang, Jianyong

AU - Xiao, Hang

AU - Bria, Alessandro

AU - Zhou, Jianlong

AU - Butler, Victoria

AU - Zhou, Zhi

AU - Gonzalez-Bellido, Paloma T.

AU - Oh, Seung W.

AU - Chen, Jichao

AU - Mitra, Ananya

AU - Tsien, Richard W.

AU - Zeng, Hongkui

AU - Ascoli, Giorgio A.

AU - Iannello, Giulio

AU - Hawrylycz, Michael

AU - Myers, Eugene

AU - Long, Fuhui

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N2 - 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.

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

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Bibliographical note

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