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

Nature Methods volume 12, pages 480481 (2015) | Download Citation

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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.

Author information

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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Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Loic A Royer.

Supplementary information

PDF files

  1. 1.

    Supplementary Texts and Figures

    Supplementary Notes 1 and 2

Videos

  1. 1.

    Supplementary Video 1

    C/C++ interface. Demonstrating how to use ClearVolume binding to C/C++ to visualize a live stream of volumetric data.

  2. 2.

    Supplementary Video 2

    LabVIEW interface. Demonstrating how to use ClearVolume binding to LabVIEW to visualize volumetric data.

  3. 3.

    Supplementary Video 3

    Python interface. Demonstrating how to use ClearVolume binding to Python to visualize volumetric data.

  4. 4.

    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.

  5. 5.

    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.

  6. 6.

    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.

  7. 7.

    Supplementary Video 7

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

  8. 8.

    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).

  9. 9.

    Supplementary Video 9

    Live sharpness estimation. ClearVolume utilizing the Tenengrad image sharpness measure to provide audiovisual feedback on PSF quality.

  10. 10.

    Supplementary Video 10

    Live drift correction. ClearVolume visualizing sample drift inside the imaging volume using simulated drift data.

  11. 11.

    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.

  12. 12.

    Supplementary Video 12

    Fiji interface. Demonstrating the integration of ClearVolume into Fiji.

  13. 13.

    Supplementary Video 13

    Remote connection inside Fiji. Demonstrating how to fetch remote data via ClearVolume for processing inside Fiji.

  14. 14.

    Supplementary Video 14

    KNIME interface. Demonstrating the integration of ClearVolume into KNIME.

About this article

Publication history

Published

DOI

https://doi.org/10.1038/nmeth.3372

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