DeepSTORM3D: dense 3D localization microscopy and PSF design by deep learning


An outstanding challenge in single-molecule localization microscopy is the accurate and precise localization of individual point emitters in three dimensions in densely labeled samples. One established approach for three-dimensional single-molecule localization is point-spread-function (PSF) engineering, in which the PSF is engineered to vary distinctively with emitter depth using additional optical elements. However, images of dense emitters, which are desirable for improving temporal resolution, pose a challenge for algorithmic localization of engineered PSFs, due to lateral overlap of the emitter PSFs. Here we train a neural network to localize multiple emitters with densely overlapping Tetrapod PSFs over a large axial range. We then use the network to design the optimal PSF for the multi-emitter case. We demonstrate our approach experimentally with super-resolution reconstructions of mitochondria and volumetric imaging of fluorescently labeled telomeres in cells. Our approach, DeepSTORM3D, enables the study of biological processes in whole cells at timescales that are rarely explored in localization microscopy.

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Fig. 1: Optical setup and approach overview.
Fig. 2: Comparison to MP.
Fig. 3: Super-resolution 3D imaging over a 4 μm z range.
Fig. 4: PSF learning for high-density 3D imaging.
Fig. 5: Three-dimensional imaging of telomeres in a single snapshot.
Fig. 6: Volumetric tracking of telomeres in live MEF cells.

Data availability

The data that support the findings of this study are available from the corresponding author upon reasonable request.

Code availability

Code is made publicly available at

Change history

  • 26 June 2020

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.


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We thank the Garini laboratory (Bar-Ilan University) for the U2OS cells, lmna−/− MEFs and the plasmid encoding for DsRed-hTRF1. We thank J. Ries for help with the application of SMAP-2018 to Tetrapod PSFs. We gratefully acknowledge the support of the NVIDIA Corporation with the donation of the Titan V GPU used for this research. We thank the staff of the Micro-Nano-Fabrication and Printing Unit at the Technion for their assistance with the phase mask fabrication. We thank Google for the research cloud units provided to accelerate this research. E.N., O.A., B.F. and R.O. are supported by H2020 European Research Council Horizon 2020 (802567); T.M. is supported by the Israel Science Foundation (grant no. 852/17) and by the Ollendorff Foundation; R.G. and O.A. are supported by the Israel Science Foundation (grant no. 450/18); Y.S. is supported by the Technion-Israel Institute of Technology Career Advancement Chairship; L.E.W. and Y.S. are supported by the Zuckerman Foundation. D.F. is supported by Google.

Author information




E.N., D.F., T.M. and Y.S. conceived the approach. E.N. performed the simulations and analyzed the data with contributions from all authors. E.N., R.G., B.F., L.E.W., O.A. and T.N. collected the data. R.O. fabricated the physical phase mask. T.N. prepared MEF cells. E.N., D.F., L.E.W., T.M. and Y.S. wrote the paper with contributions from all authors.

Corresponding author

Correspondence to Yoav Shechtman.

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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 information

Supplementary Information

Supplementary Notes 1–14.

Reporting Summary

Supplementary Video 1

Localizations overlaid on experimental frames. This movie shows 70 representative experimental frames followed by an overlay of their regenerated images using the recovered 3D positions by the CNN (Fig. 3a in the main text). Note that the experimental frames are shown before and after the regenerated images for ease of visualization. The STORM experiment was repeated three times, twice analyzing 20,000 frames of two different cells from the same cell culture and once analyzing 10,000 frames of a cell from a different cell culture all leading to similar performance. Scale bar, 5 μm.

Supplementary Video 2

Rotating 3D rendering of the recovered mitochondria. This movie shows a 3D rendering of the super-resolved mitochondria spanning a 4-μm axial range (Fig. 3b in the main text). The z range is rendered with a scaling factor of 2 to ease axial visualization. Scale bar, 5 μm.

Supplementary Video 3

Sweep through the axial slices of the recovered mitochondria. This movie shows a sweep through 33 nm axial slices of the rendered 3D histogram for the mitochondria data (Fig. 3b in the main text). Scale bar, 5 μm.

Supplementary Video 4

Phase mask learning via backpropagation. This movie shows the phase mask (left) and the corresponding PSF (right) being learned over training iterations (Fig. 4c in the main text). Note that the phase mask is initialized to zero modulation, meaning the standard microscope PSF. Scale bar, 2 μm.

Supplementary Video 5

Rotating Telomere z stack without a mask. This movie shows a 3D rendering of the telomere data z stack without the application of a phase mask (Fig. 5b in the main text). As clearly shown in the rendered PSFs, the telomeres exhibit different sizes and intensities. The experiment was repeated independently for n = 10 U2OS cells all showing similar characteristics. Scale bar, 5 μm.

Supplementary Video 6

Super-critical angle fluorescence (SAF) light effect on the learned PSF. This movie shows the effect of the SAF light on the experimental PSF with the learned phase mask. Upper panel shows the experimental PSF (left), the result of VIPR45, the vectorial model assuming dipole emission, and the scalar model assuming isotropic emission. The lower panel shows the difference from the experimental measurement for each model. The SAF light effect is indicated in the middle of the axial range with a red arrow. Scale bar, 2 μm.

Supplementary Video 7

Volumetric tracking of telomeres in MEF cells. This movie shows 3D tracking of telomeres in live MEF cells over a period of 50 s using the learned phase mask (Fig. 6a in the main text). White sticks point to the emitter being tracked. Time is encoded in color. The results indicate that individual telomeres exhibit different types of movements. The experiment was repeated independently for n = 10 MEF cells all showing similar characteristics and performance. Scale bar, 2 μm.

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Nehme, E., Freedman, D., Gordon, R. et al. DeepSTORM3D: dense 3D localization microscopy and PSF design by deep learning. Nat Methods 17, 734–740 (2020).

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