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ClearVolume: open-source live 3D visualization for light-sheet microscopy

Nature Methods volume 12, pages 480–481 (2015)Cite this article

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Current state-of-the-art light-sheet microscopes rely on sophisticated control software to perform the acquisition of gigabytes of image data per second over the course of hours or even days. Typically the microscopes acquire data in a first step, and in a second step these data are processed and visualized offline. The delay between data acquisition and data assessment wastes time and storage space. Technology that enables viewing and assessing data during imaging would offer significant advantages. However, even the most advanced microscopes display only the latest image plane acquired or projection while the raw volumetric data are saved to disk1,2,3,4.

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Figure 1: ClearVolume: an open-source real-time multichannel 3D visualization toolkit for microscopy.

References

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Acknowledgements

Thanks to M. Sarov of the TransgeneOmics facility (MPI-CBG) for providing C. elegans lines. Thanks to C. Schmied (MPI-CBG) for providing us with D. melanogaster embryo samples. Thanks to P. Tomancak, E. Betzig and S. Saalfeld for advice. Thanks to S. Bundschuh and the Light Microscopy Facility (MPI-CBG). This work was supported by the German Federal Ministry of Research and Education (BMBF) under the funding code 031A099.

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Authors and Affiliations

  1. Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

    Loic A Royer, Martin Weigert, Ulrik Günther, Nicola Maghelli, Florian Jug, Ivo F Sbalzarini & Eugene W Myers

  2. Center for Systems Biology Dresden, Dresden, Germany

    Loic A Royer, Martin Weigert, Ulrik Günther, Nicola Maghelli, Florian Jug, Ivo F Sbalzarini & Eugene W Myers

  3. Faculty of Computer Science, Technische Universität Dresden, Dresden, Germany

    Ulrik Günther, Ivo F Sbalzarini & Eugene W Myers

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  1. Loic A Royer
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  2. Martin Weigert
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  3. Ulrik Günther
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Correspondence to Loic A Royer.

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Supplementary information

Supplementary Texts and Figures

Supplementary Notes 1 and 2 (PDF 4120 kb)

Supplementary Video 1

C/C++ interface. Demonstrating how to use ClearVolume binding to C/C++ to visualize a live stream of volumetric data. (MP4 2213 kb)

Supplementary Video 2

LabVIEW interface. Demonstrating how to use ClearVolume binding to LabVIEW to visualize volumetric data. (MP4 5368 kb)

Supplementary Video 3

Python interface. Demonstrating how to use ClearVolume binding to Python to visualize volumetric data. (MP4 7072 kb)

Supplementary Video 4

Live 3D acquisition and view of a C. elegans embryo (His-GFP+BTub-GFP). The embryo is at the AB8 stage, 50 minutes after first division of the AB founder cell. We see 12 cells, two of which are undergoing mitosis (MS and E founder cells) . We used our high-speed light sheet microscope capable acquiring 6 stacks per second. In a second part the video shows a full screen view of the same embryo where we center, zoom and rotate around a cell division. In a third part the video shows the same embryo imaged at a later stage. (MP4 7137 kb)

Supplementary Video 5

Remote connection to an OpenSPIM microscope augmented with ClearVolume. The microscope is recording a time lapse of the development of a Drosophila melanogaster (histone-YFP) embryo (time point period: 5 min). We show it is possible to remotely access and visualize a 3D stack. (MP4 4406 kb)

Supplementary Video 6

Time-shift feature on an OpenSPIM microscope. The screen recording shows a time lapse recording of the development of a Drosophila melanogaster (Histone-YFP) embryo (acquisition time step: 5 min), and the replay using the time-shift feature of ClearVolume. (MP4 4840 kb)

Supplementary Video 7

Visualizing the 3D point spread function. Visualization and inspection of the 3D PSF of a light-sheet microscope using ClearVolume. (MP4 6912 kb)

Supplementary Video 8

Gaussian and Bessel beam visualization. Visualization and inspection of the full 3D structure of Gaussian and Bessel beams in a digital scanned light sheet microscope (DSLM). (MP4 8747 kb)

Supplementary Video 9

Live sharpness estimation. ClearVolume utilizing the Tenengrad image sharpness measure to provide audiovisual feedback on PSF quality. (MP4 4548 kb)

Supplementary Video 10

Live drift correction. ClearVolume visualizing sample drift inside the imaging volume using simulated drift data. (MP4 5757 kb)

Supplementary Video 11

Beyond light-sheet microscopes. ClearVolume visualizing live data acquired on a commercial Zeiss LSM 780 NLO confocal microscope via the pyclearvolume extension. (MP4 5611 kb)

Supplementary Video 12

Fiji interface. Demonstrating the integration of ClearVolume into Fiji. (MP4 10692 kb)

Supplementary Video 13

Remote connection inside Fiji. Demonstrating how to fetch remote data via ClearVolume for processing inside Fiji. (MP4 5405 kb)

Supplementary Video 14

KNIME interface. Demonstrating the integration of ClearVolume into KNIME. (MP4 6842 kb)

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Royer, L., Weigert, M., Günther, U. et al. ClearVolume: open-source live 3D visualization for light-sheet microscopy. Nat Methods 12, 480–481 (2015). https://doi.org/10.1038/nmeth.3372

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