DOI: 10.1038/s41598-018-25922-7. Accurate and fiducial-marker-free correction for three-dimensional chromatic shift in biological fluorescence microscopy

Accurate and fiducial-marker-free correction for three-dimensional chromatic shift in biological fluorescence microscopy

10.1038/s41598-018-25922-7

Crossref journal-article

Springer Science and Business Media LLC

Scientific Reports (297)

Abstract

AbstractCorrection of chromatic shift is necessary for precise registration of multicolor fluorescence images of biological specimens. New emerging technologies in fluorescence microscopy with increasing spatial resolution and penetration depth have prompted the need for more accurate methods to correct chromatic aberration. However, the amount of chromatic shift of the region of interest in biological samples often deviates from the theoretical prediction because of unknown dispersion in the biological samples. To measure and correct chromatic shift in biological samples, we developed a quadrisection phase correlation approach to computationally calculate translation, rotation, and magnification from reference images. Furthermore, to account for local chromatic shifts, images are split into smaller elements, for which the phase correlation between channels is measured individually and corrected accordingly. We implemented this method in an easy-to-use open-source software package, calledChromagnon, that is able to correct shifts with a 3D accuracy of approximately 15 nm. Applying this software, we quantified the level of uncertainty in chromatic shift correction, depending on the imaging modality used, and for different existing calibration methods, along with the proposed one. Finally, we provide guidelines to choose the optimal chromatic shift registration method for any given situation.

Bibliography

Matsuda, A., Schermelleh, L., Hirano, Y., Haraguchi, T., & Hiraoka, Y. (2018). Accurate and fiducial-marker-free correction for three-dimensional chromatic shift in biological fluorescence microscopy. Scientific Reports, 8(1).

Authors 5

Atsushi Matsuda (first)
Lothar Schermelleh (additional)
Yasuhiro Hirano (additional)
Tokuko Haraguchi (additional)
Yasushi Hiraoka (additional)

References 25 Referenced 57

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Hell, S. W. Nanoscopy with Focused Light (Nobel Lecture). Angew. Chem. Int. Ed. 54, 8054–8066 (2015). (10.1002/anie.201504181) / Angew. Chem. Int. Ed. by SW Hell (2015)
Moerner, W. E. Single-Molecule Spectroscopy, Imaging, and Photocontrol: Foundations for Super-Resolution Microscopy (Nobel Lecture). Angew. Chem. Int. Ed. 54, 8067–8093 (2015). (10.1002/anie.201501949) / Angew. Chem. Int. Ed. by WE Moerner (2015)
Manders, E. M. M. Chromatic shift in multicolour confocal microscopy. J. Microsc. 185, 321–328 (1997). (10.1046/j.1365-2818.1997.d01-625.x) / J. Microsc. by EMM Manders (1997)
Koyama-Honda, I. et al. Fluorescence Imaging for Monitoring the Colocalization of Two Single Molecules in Living Cells. Biophys. J. 88, 2126–2136 (2005). (10.1529/biophysj.104.048967) / Biophys. J. by I Koyama-Honda (2005)
Churchman, L. S., Ökten, Z., Rock, R. S., Dawson, J. F. & Spudich, J. A. Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time. Proc. Natl. Acad. Sci. USA 102, 1419–1423 (2005). (10.1073/pnas.0409487102) / Proc. Natl. Acad. Sci. USA by LS Churchman (2005)
Pertsinidis, A., Zhang, Y. & Chu, S. Subnanometre single-molecule localization, registration and distance measurements. Nature 466, 647–651 (2010). (10.1038/nature09163) / Nature by A Pertsinidis (2010)
Eliscovich, C., Shenoy, S. M. & Singer, R. H. Imaging mRNA and protein interactions within neurons. Proc. Natl. Acad. Sci. 114, E1875–E1884 (2017). (10.1073/pnas.1621440114) / Proc. Natl. Acad. Sci. by C Eliscovich (2017)
Erdelyi, M. et al. Correcting chromatic offset in multicolor super-resolution localization microscopy. Opt. Express 21, 10978–10988 (2013). (10.1364/OE.21.010978) / Opt. Express by M Erdelyi (2013)
Gahlmann, A. et al. Quantitative Multicolor Subdiffraction Imaging of Bacterial Protein Ultrastructures in Three Dimensions. Nano Lett. 13, 987–993 (2013). (10.1021/nl304071h) / Nano Lett. by A Gahlmann (2013)
Bates, M., Dempsey, G. T., Chen, K. H. & Zhuang, X. Multicolor Super-Resolution Fluorescence Imaging via Multi-Parameter Fluorophore Detection. ChemPhysChem 13, 99–107 (2012). (10.1002/cphc.201100735) / ChemPhysChem by M Bates (2012)
Kraus, F. et al. Quantitative 3D structured illumination microscopy of nuclear structures. Nat Protoc 2, 1011–1028 (2017). (10.1038/nprot.2017.020) / Nat Protoc by F Kraus (2017)
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Zitová, B. & Flusser, J. Image registration methods: a survey. Image Vis. Comput. 21, 977–1000 (2003). (10.1016/S0262-8856(03)00137-9) / Image Vis. Comput. by B Zitová (2003)
Wolberg, G. & Zokai, S. Robust image registration using log-polar transform. In Proceedings 2000 International Conference on Image Processing (Cat. No. 00CH37101) 1, 493–496 vol.1 (2000). (10.1109/ICIP.2000.901003)
Holia, M. S. & Thakar, V. K. Image Registration for Recovering Affine Transformation Using Nelder Mead Simplex Method for Optimization. Int. J. Image Process. 3, 218–228 (2009). / Int. J. Image Process. by MS Holia (2009)
Simper, A. Correcting general band-to-band misregistrations. In, International Conference on Image Processing, 1996. Proceedings 1, 597–600 vol. 2 (1996). (10.1109/ICIP.1996.560932)
Schermelleh, L. et al. Subdiffraction Multicolor Imaging of the Nuclear Periphery with 3D Structured Illumination Microscopy. Science 320, 1332–1336 (2008). (10.1126/science.1156947) / Science by L Schermelleh (2008)
Gustafsson, M. G. L. et al. Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination. Biophys. J. 94, 4957–4970 (2008). (10.1529/biophysj.107.120345) / Biophys. J. by MGL Gustafsson (2008)
Demmerle, J. et al. Strategic and practical guidelines for successful structured illumination microscopy. Nat Protoc 12, 988–1010 (2017). (10.1038/nprot.2017.019) / Nat Protoc by J Demmerle (2017)
Gómez-Saldivar, G. et al. Identification of Conserved MEL-28/ELYS Domains with Essential Roles in Nuclear Assembly and Chromosome Segregation. PLOS Genet. 12, e1006131 (2016). (10.1371/journal.pgen.1006131) / PLOS Genet. by G Gómez-Saldivar (2016)
Kumeta, M., Hirai, Y., Yoshimura, S. H., Horigome, T. & Takeyasu, K. Antibody-based analysis reveals ‘filamentous vs. non-filamentous’ and ‘cytoplasmic vs. nuclear’ crosstalk of cytoskeletal proteins. Exp. Cell Res. 319, 3226–3237 (2013). (10.1016/j.yexcr.2013.07.021) / Exp. Cell Res. by M Kumeta (2013)
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Dates

Type	When
Created	7 years, 3 months ago (May 9, 2018, 7:34 a.m.)
Deposited	1 month, 2 weeks ago (July 4, 2025, 7:33 a.m.)
Indexed	1 week, 2 days ago (Aug. 12, 2025, 5:41 p.m.)
Issued	7 years, 3 months ago (May 15, 2018)
Published	7 years, 3 months ago (May 15, 2018)
Published Online	7 years, 3 months ago (May 15, 2018)

Funders 0

None

BibTeX

@article{Matsuda_2018, title={Accurate and fiducial-marker-free correction for three-dimensional chromatic shift in biological fluorescence microscopy}, volume={8}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-018-25922-7}, DOI={10.1038/s41598-018-25922-7}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Matsuda, Atsushi and Schermelleh, Lothar and Hirano, Yasuhiro and Haraguchi, Tokuko and Hiraoka, Yasushi}, year={2018}, month=may }

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