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Nature Methods
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Software for bead-based registration of selective plane illumination microscopy data

Nature Methodsvolume 7, pages418–419 (2010)Cite this article

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To the Editor:

SPIM multiview registration is complicated by degradation of the signal along the illumination as well as detection axes (Fig. 1b), limited overlap between the views, different orientations of the optical sections and development of the specimen during acquisition. We developed a SPIM registration method and implemented it in a plugin for Fiji. The software enables efficient, sample-independent registration of multiview SPIM acquisitions using fluorescent beads in rigid mounting medium as fiduciary markers.

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Figure 1: Bead-based registration framework.

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Acknowledgements

We thank Carl Zeiss Microimaging for access to the SPIM demonstrator; R.K. Ejsmont (Max Planck Institute of Molecular Cell Biology and Genetics, Dresden) for His-YFP flies; D. White, E. Dimitrova, M. Sarov and P. Campinho for help with imaging and B. Schmid for help with 3D viewer programming. S.P. and S.S. were supported by a Dresden International Graduate School for Biomedicine and Bioengineering doctorate stipend. J.S. and P.T. acknowledge funding from the Human Frontier Science Program Research grant RGY0084.

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Author notes

  1. Stephan Preibisch and Stephan Saalfeld: These authors contributed equally to this work.

Authors and Affiliations

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

    Stephan Preibisch, Stephan Saalfeld, Johannes Schindelin & Pavel Tomancak

Authors
  1. Stephan Preibisch

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  2. Stephan Saalfeld

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  3. Johannes Schindelin

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  4. Pavel Tomancak

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Corresponding author

Correspondence toPavel Tomancak.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8, Supplementary Table 1, Supplementary Methods, Supplementary Data (PDF 4604 kb)

Supplementary Software

SPIM registration plugin for Fiji. (ZIP 4350 kb)

Supplementary Video 1

Rotation capabilities of the selective plane illumination microscope. (MOV 42 kb)

Supplementary Video 2

Visualization of the global optimization of eight view selective plane illumination microscope acquisition ofC. elegans with 40×, 0.8 objective. (MOV 4043 kb)

Supplementary Video 3

Visualization of the global optimization of tiled single-photon confocal acquisition ofDrosophila with 40×, 0.8 objective. (MOV 6422 kb)

Supplementary Video 4

Three-dimensional rendering ofDrosophila gastrulation time-lapse acquired from seven angles. (MOV 393 kb)

Supplementary Video 5

Three-dimensional rendering ofDrosophila embryogenesis time-lapse acquired from five angles. (MOV 5121 kb)

Supplementary Video 6

Three-dimensional rendering of fixedDrosophila reconstructed from multiview spinning disc acquisition. (MOV 1108 kb)

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Preibisch, S., Saalfeld, S., Schindelin, J.et al. Software for bead-based registration of selective plane illumination microscopy data.Nat Methods7, 418–419 (2010). https://doi.org/10.1038/nmeth0610-418

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