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Tutorial: avoiding and correcting sample-induced spherical aberration artifacts in 3D fluorescence microscopy

A Publisher Correction to this article was published on 02 December 2020

This article has been updated


Spherical aberration (SA) occurs when light rays entering at different points of a spherical lens are not focused to the same point of the optical axis. SA that occurs inside the lens elements of a fluorescence microscope is well understood and corrected for. However, SA is also induced when light passes through an interface of refractive index (RI)-mismatched substances (i.e., a discrepancy between the RI of the immersion medium and the RI of the sample). SA due to RI mismatches has many deleterious effects on imaging. Perhaps most important for 3D imaging is that the distance the image plane moves in a sample is not equivalent to the distance traveled by an objective (or stage) during z-stack acquisition. This non-uniform translation along the z axis gives rise to artifactually elongated images (if the objective is immersed in a medium with a higher RI than that of the sample) or compressed images (if the objective is immersed in a medium with a lower RI than that of the sample) and alters the optimal axial sampling rate. In this tutorial, we describe why this distortion occurs, how it impacts quantitative measurements and axial resolution, and what can be done to avoid SA and thereby prevent distorted images. In addition, this tutorial aims to better inform researchers of how to correct RI mismatch–induced axial distortions and provides a practical ImageJ/Fiji-based tool to reduce the prevalence of volumetric measurement errors and lost axial resolution.

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Fig. 1: Refractive index mismatches induce spherical aberration and axial distortion.
Fig. 2: Comparison of methods for determining refractive index–mismatch correction factors (high to low refractive index).
Fig. 3: Comparison of methods for determining refractive index mismatch correction factors (low to high refractive index).
Fig. 4: Refractive index mismatches induce a focal shift.
Fig. 5: Refractive index mismatches induce spherical aberration and axial distortion.
Fig. 6: Correcting axial sampling improves segmentation.

Data availability

All original (raw) data are available from the authors upon reasonable request.

Code availability

All necessary code and instructions for running the axial correction macro are provided in the Supplementary Software and Box 1.

Change history

  • 02 December 2020

    A Correction to this paper has been published:


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We thank S. Piccinotti and L. Rubin for providing organoid samples. We thank the Harvard Center for Biological Imaging for infrastructure and support. J.W.L. was supported by the following funding sources: National Institutes of Health grants P50 MH094271, U24 NS109102, and U19 NS104653 and Department of Defense MURI award GG008784.

Author information




The idea for calculating axial distortion correction factors as described in this tutorial was conceived by D.S.R. and J.W.L. E.E.D. and D.S.R. carried out experiments and analyzed data. D.S.R., J.W.L. and E.E.D. wrote the manuscript. All authors contributed to editing the final manuscript.

Corresponding author

Correspondence to Douglas S. Richardson.

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The authors declare no competing interests.

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Peer review information Nature Protocols thanks Chrysanthe Preza and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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References that contributed to the development of this protocol

Visser, T. D. et al. Optik 90, 17–19 (1992):

Hell, S., Reiner, G., Cremer, C. & Stelzer, E. H. K. J. Microsc. 169, 391–405, (1993):

Supplementary information

Supplementary Information

Supplementary Methods and Supplementary Notes 1 and 2.

Reporting Summary

Supplementary Software

Supplementary Software

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Diel, E.E., Lichtman, J.W. & Richardson, D.S. Tutorial: avoiding and correcting sample-induced spherical aberration artifacts in 3D fluorescence microscopy. Nat Protoc 15, 2773–2784 (2020).

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