BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples (original) (raw)

References

  1. Chung, K. et al. Nature 497, 332–337 (2013).
    Article CAS Google Scholar
  2. Chen, F., Tillberg, P. W. & Boyden, E. S. Science 347, 543–548 (2015).
    Article CAS Google Scholar
  3. Huisken, J., Swoger, J., Del Bene, F., Wittbrodt, J. & Stelzer, E. H. K. Science 305, 1007–1009 (2004).
    Article CAS Google Scholar
  4. Chhetri, R. K. et al. Nat. Methods 12, 1171–1178 (2015).
    Article CAS Google Scholar
  5. Huisken, J. & Stainier, D. Y. R. Opt. Lett. 32, 2608–2610 (2007).
    Article Google Scholar
  6. Tomer, R., Ye, L., Hsueh, B. & Deisseroth, K. Nat. Protoc. 9, 1682–1697 (2014).
    Article CAS Google Scholar
  7. Richardson, D. S. & Lichtman, J. W. Cell 162, 246–257 (2015).
    Article CAS Google Scholar
  8. Pietzsch, T., Saalfeld, S., Preibisch, S. & Tomancak, P. Nat. Methods 12, 481–483 (2015).
    Article CAS Google Scholar
  9. Linkert, M. et al. J. Cell Biol. 189, 777–782 (2010).
    Article CAS Google Scholar
  10. Pietzsch, T., Preibisch, S., Tomancák, P. & Saalfeld, S. Bioinformatics 28, 3009–3011 (2012).
    Article CAS Google Scholar
  11. Kuglin, C. D. & Hines, D. C. in Proc. IEEE International Conference on Cybernetics and Society 163–165 (IEEE, 1975)
  12. Preibisch, S., Saalfeld, S. & Tomancák, P. Bioinformatics 25, 1463–1465 (2009).
    Article CAS Google Scholar
  13. Emmenlauer, M. et al. J. Microsc. 233, 42–60 (2009).
    Article CAS Google Scholar
  14. Chalfoun, J. et al. Sci. Rep. 7, 4988 (2017).
    Article Google Scholar
  15. Saalfeld, S., Fetter, R., Cardona, A. & Tomancák, P. Nat. Methods 9, 717–720 (2012).
    Article CAS Google Scholar
  16. Bria, A. & Ianello, G. BMC Bioinformatics 13, 316 (2012).
    Article Google Scholar
  17. Besl, P. J. & McKay, N. D. IEEE Trans. Pattern Anal. Mach. Intell. 14, 239–256 (1992).
    Article Google Scholar
  18. Migliori, B. et al. BMC Biol. 16, 57 (2018).
    Article Google Scholar
  19. Schaefer, S., McPhail, T. & Warren, J. ACM Trans. Graph. 25, 533–540 (2006).
    Article Google Scholar
  20. Ryan, D. P. et al. Nat. Commun. 8, 612 (2017).
    Article Google Scholar
  21. Royer, L. A. et al. Adaptive light-sheet microscopy for long-term, high-resolution imaging in living organisms. Nat. Biotechnol. 34, 1267–1278 (2016).
    Article CAS Google Scholar
  22. Nieuwenhuizen, R. P. J. et al. Nat. Methods 10, 557–562 (2013).
    Article CAS Google Scholar
  23. Preibisch, S. et al. Nat. Methods 11, 645–648 (2014).
    Article CAS Google Scholar
  24. Gao, R. et al. Science 363, eaau8302 (2019).
    Article Google Scholar
  25. Schindelin, J. et al. Nat. Methods 9, 676–682 (2012).
    Article CAS Google Scholar
  26. Sakkou, M. et al. Cell Metab. 5, 450–463 (2007).
    Article CAS Google Scholar
  27. Nguyen, J. P., Linder, A. N., Plummer, G. S., Shaevitz, J. W. & Leifer, A. M. PLoS Comput. Biol. 13, e1005517 (2017).
    Article Google Scholar
  28. Karp, X. in WormBook (ed. The C. elegans Research Community, 2016); https://doi.org/10.1895/wormbook.1.180.1
  29. Pfeiffer, D. B. et al. Proc. Natl Acad. Sci. USA 105, 9715–9720 (2008).
    Article CAS Google Scholar
  30. Tillberg, P. W. et al. Nat. Biotechnol. 34, 987–992 (2016).
    Article CAS Google Scholar
  31. Preibisch, S., Saalfeld, S., Schindelin, J. & Tomancák, P. Nat. Methods 7, 418–419 (2010).
    Article CAS Google Scholar
  32. Smith, C. S. et al. J. Cell Biol. 209, 609–619 (2015).
    Article CAS Google Scholar
  33. Lowe, D. G. Int. J. Comput. Vis. 60, 91–110 (2004).
    Article Google Scholar
  34. Matsuda, A., Schermelleh, L., Hirano, Y., Haraguchi, T. & Hiraoka, Y. Sci. Rep. 8, 7583 (2018).
    Article Google Scholar
  35. Weigert, M., Subramanian, K., Bundschuh, S. T., Myers, E. W. & Kreysing, M. PLoS Comput. Biol. 14, e1006079 (2018).
    Article Google Scholar
  36. Fischler, M. A. & Bolles, R. C. Commun. ACM 24, 381–395 (1981).
    Article Google Scholar
  37. Cleveland, W. S. J. Am. Stat. Assoc. 74, 829–836 (1979).
    Article Google Scholar
  38. 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).
  39. Blasse, C. et al. Bioinformatics 33, 2563–2569 (2017).
    Article CAS Google Scholar
  40. Schmied, C., Steinbach, P., Pietzsch, T., Preibisch, S. & Tomancák, P. Bioinformatics 32, 1112–1114 (2016).
    Article CAS Google Scholar

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