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PYMEVisualize: an open-source tool for exploring 3D super-resolution data

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Fig. 1: Overview of PYMEVisualize.

Data availability

The data used to generate the figures in this paper are available from the corresponding author on reasonable request.

Code availability

Source code for PYMEVisualize is available at https://github.com/python-microscopy/python-microscopy. Compiled packages can be downloaded from https://python-microscopy.org/downloads/. For installation guidance, see Supplementary Note 2.

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Acknowledgements

As a long-running project, this work has received funding from a range of sources including the NIH (R01 GM118486-02,U01EB021232), the Wellcome Trust (203285/B/16/Z), the Engineering and Physical Sciences Research Council of the UK (EP/N008235/1), the Health Research Council (New Zealand) and Marsden Fund (New Zealand). The authors thank Yongdeng Zhang and Lena Schroeder for generating the endoplasmic reticulum and mitochondrial and the microtubule and OMP25 datasets, and thank Yongdeng Zhang, Mengyuan Sun, Ben Rollins and Joerg Bewersdorf for discussions.

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Authors and Affiliations

  1. Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand

    Zach Marin & David Baddeley

  2. Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA

    Zach Marin, Michael Graff, Andrew E. S. Barentine, Kenny Kwok Hin Chung, Lukas A. Fuentes & David Baddeley

  3. Department of Biomedical Engineering, Yale University, New Haven, CT, USA

    Zach Marin & Andrew E. S. Barentine

  4. Living Systems Institute and Biomedical Physics, University of Exeter, Exeter, UK

    Christian Soeller

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  1. Zach Marin
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  2. Michael Graff
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  3. Andrew E. S. Barentine
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  4. Christian Soeller
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  5. Kenny Kwok Hin Chung
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  6. Lukas A. Fuentes
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  7. David Baddeley
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Contributions

D.B. created the PYME package. Z.M., M.G., K.K.H.C., C.S., A.E.S.B. and D.B. contributed to the codebase. L.A.F. suggested features and usability improvements, and tested the software extensively. All authors contributed to the writing of this manuscript.

Corresponding author

Correspondence to David Baddeley.

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Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature Methods thanks Dylan Owen and Nico Stuurman for their contribution to the peer review of this work.

Supplementary information

Supplementary Information

Supplementary Notes 1–3

Reporting Summary

Supplementary Video 1

A pipeline for visualizing mesh representations of super-resolution data.

Supplementary Video 2

A pipeline for quantifying super-resolution data of RyR and junctophilin.

Supplementary Data

Example endoplasmic reticulum super-resolution data for Supplementary Note 1.

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Marin, Z., Graff, M., Barentine, A.E.S. et al. PYMEVisualize: an open-source tool for exploring 3D super-resolution data. Nat Methods 18, 582–584 (2021). https://doi.org/10.1038/s41592-021-01165-9

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