Light-sheet imaging of cleared and expanded samples creates terabyte-sized datasets that consist of many unaligned three-dimensional image tiles, which must be reconstructed before analysis. We developed the BigStitcher software to address this challenge. BigStitcher enables interactive visualization, fast and precise alignment, spatially resolved quality estimation, real-time fusion and deconvolution of dual-illumination, multitile, multiview datasets. The software also compensates for optical effects, thereby improving accuracy and enabling subsequent biological analysis.
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Small example datasets are available for download from the Open Science Foundation at https://osf.io/bufza/. Larger datasets are available on request. Additional datasets uploaded at a later stage will be linked from the documentation page which can be found at https://imagej.net/BigStitcher#Example_Datasets. Example datasets are explained in detail in Supplementary Note 18.
All source code used in this publication (BigStitcher, phase correlation simulation and benchmarks, and the simulation of light propagation in tissue using ray tracing) is open-source and published under the GNU General Public License version 2. The latest stable releases used in this publication are provided as Supplementary Software; current versions that include bugfixes and updates can be downloaded from GitHub (at https://github.com/PreibischLab/BigStitcher; https://github.com/PreibischLab/multiview-reconstruction; and https://github.com/PreibischLab/multiview-simulation; see Supplementary Notes 19 and 20 for further explanations). Details on how to use the software are described in Supplementary Note 21.
Chung, K. et al. Nature 497, 332–337 (2013).
Chen, F., Tillberg, P. W. & Boyden, E. S. Science 347, 543–548 (2015).
Huisken, J., Swoger, J., Del Bene, F., Wittbrodt, J. & Stelzer, E. H. K. Science 305, 1007–1009 (2004).
Chhetri, R. K. et al. Nat. Methods 12, 1171–1178 (2015).
Huisken, J. & Stainier, D. Y. R. Opt. Lett. 32, 2608–2610 (2007).
Tomer, R., Ye, L., Hsueh, B. & Deisseroth, K. Nat. Protoc. 9, 1682–1697 (2014).
Richardson, D. S. & Lichtman, J. W. Cell 162, 246–257 (2015).
Pietzsch, T., Saalfeld, S., Preibisch, S. & Tomancak, P. Nat. Methods 12, 481–483 (2015).
Linkert, M. et al. J. Cell Biol. 189, 777–782 (2010).
Pietzsch, T., Preibisch, S., Tomancák, P. & Saalfeld, S. Bioinformatics 28, 3009–3011 (2012).
Kuglin, C. D. & Hines, D. C. in Proc. IEEE International Conference on Cybernetics and Society 163–165 (IEEE, 1975)
Preibisch, S., Saalfeld, S. & Tomancák, P. Bioinformatics 25, 1463–1465 (2009).
Emmenlauer, M. et al. J. Microsc. 233, 42–60 (2009).
Chalfoun, J. et al. Sci. Rep. 7, 4988 (2017).
Saalfeld, S., Fetter, R., Cardona, A. & Tomancák, P. Nat. Methods 9, 717–720 (2012).
Bria, A. & Ianello, G. BMC Bioinformatics 13, 316 (2012).
Besl, P. J. & McKay, N. D. IEEE Trans. Pattern Anal. Mach. Intell. 14, 239–256 (1992).
Migliori, B. et al. BMC Biol. 16, 57 (2018).
Schaefer, S., McPhail, T. & Warren, J. ACM Trans. Graph. 25, 533–540 (2006).
Ryan, D. P. et al. Nat. Commun. 8, 612 (2017).
Royer, L. A. et al. Adaptive light-sheet microscopy for long-term, high-resolution imaging in living organisms. Nat. Biotechnol. 34, 1267–1278 (2016).
Nieuwenhuizen, R. P. J. et al. Nat. Methods 10, 557–562 (2013).
Preibisch, S. et al. Nat. Methods 11, 645–648 (2014).
Gao, R. et al. Science 363, eaau8302 (2019).
Schindelin, J. et al. Nat. Methods 9, 676–682 (2012).
Sakkou, M. et al. Cell Metab. 5, 450–463 (2007).
Nguyen, J. P., Linder, A. N., Plummer, G. S., Shaevitz, J. W. & Leifer, A. M. PLoS Comput. Biol. 13, e1005517 (2017).
Karp, X. in WormBook (ed. The C. elegans Research Community, 2016); https://doi.org/10.1895/wormbook.1.180.1
Pfeiffer, D. B. et al. Proc. Natl Acad. Sci. USA 105, 9715–9720 (2008).
Tillberg, P. W. et al. Nat. Biotechnol. 34, 987–992 (2016).
Preibisch, S., Saalfeld, S., Schindelin, J. & Tomancák, P. Nat. Methods 7, 418–419 (2010).
Smith, C. S. et al. J. Cell Biol. 209, 609–619 (2015).
Lowe, D. G. Int. J. Comput. Vis. 60, 91–110 (2004).
Matsuda, A., Schermelleh, L., Hirano, Y., Haraguchi, T. & Hiraoka, Y. Sci. Rep. 8, 7583 (2018).
Weigert, M., Subramanian, K., Bundschuh, S. T., Myers, E. W. & Kreysing, M. PLoS Comput. Biol. 14, e1006079 (2018).
Fischler, M. A. & Bolles, R. C. Commun. ACM 24, 381–395 (1981).
Cleveland, W. S. J. Am. Stat. Assoc. 74, 829–836 (1979).
Preibisch, S., Rohlfing, T., Hasak, M. P. & Tomancák, P. in Proc. of the International Society for Optics and Photonics, Medical Imaging (eds. Reinhardt, J. M. & Pluim, J. P. W.) (SPIE, 2008).
Blasse, C. et al. Bioinformatics 33, 2563–2569 (2017).
Schmied, C., Steinbach, P., Pietzsch, T., Preibisch, S. & Tomancák, P. Bioinformatics 32, 1112–1114 (2016).
We thank T. Pietzsch and S. Saalfeld for insightful discussions and BigDataViewer and ImgLib2 support; N. Vladimirov for very helpful microscopy discussions; C. Rueden for Fiji support and maintenance; N. Gompel for early-stage project discussions; and the Caenorhabditis Genetics Center at the University of Minnesota for providing C. elegans strains. S.P., F.P. and M.T. were funded by MDC Berlin; S.P. was supported by HFSP grant RGP0021/2018-102; F.P. was funded by a PhD fellowship from Studienstiftung des deutschen Volkes; F.R.R. and M.T. were funded by the Helmholtz Alliances ICEMED and AMPro; D.H., H.H. and H.L. were funded by the Deutsche Forschungsgemeinschaft (DFG, Nanosystems Initiative Munich), the NHGRI/NIH Center for Photogenomics (grant RM1 HG007743) and LMU Munich; and P.T., N.R., R.K.C., A.C. and P.J.K. were funded by HHMI Janelia.
The authors declare no competing interests.
Peer review information: Rita Strack was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.
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Supplementary Figs. 1–23, Supplementary Tables 1 and 2 and Supplementary Notes 1–21.
Interactive link verification.
Simulations of light propagation in tissue.
Interactive walk through a cleared sample.
Quality of multiview registration on the expanded sample.
3D maximum-intensity projection of the expanded sample.
Low-resolution overview of reconstructed mouse brain.
3D maximum-intensity projection of the reconstructed C. elegans dauer.
Quality measurement by rFRC (single image tile).
Quality measurement by rFRC (large sample).
Source code for BigStitcher, phase correlation simulation and benchmark, and the simulation of light propagation in tissue using ray tracing, all licensed under the GNU General Public License version 2.
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Nature Methods (2019)