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Navigate: an open-source platform for smart light-sheet microscopy

Nature Methods (2024)Cite this article

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Navigate enables biologists and technology developers alike to establish and reuse smart microscopy pipelines on diverse sets of hardware from within a single framework. While generalizable Python-based frameworks for smart microscopy have been built, they were designed for stimulated emission depletion5 or single-molecule localization microscopy6 and do not yet address LSFM’s specific acquisition challenges, including decoupled illumination and detection optomechanics and a lack of an optical substrate for focus maintenance. While GUI-based frameworks for image postprocessing exist6, to the authors’ knowledge, navigate is the only software that enables decision-based acquisition routines to be generated in a code-free format (Supplementary Table 1).

A schematic of navigate’s software architecture is presented in Supplementary Fig. 1. The plug-in architecture of navigate facilitates the addition of new hardware, enabling users to integrate otherwise unsupported devices. For image-based feedback, custom analysis routines can also be loaded within navigate’s environment to evaluate images stored as NumPy arrays in memory. Navigate supports the addition of REST-API interfaces for two-way communication with image analysis programs running outside of Python or in different Python environments, such as Ilastik7, enabling developers to make calls to state-of-the-art software while avoiding dependency conflicts. Image-based feedback can be leveraged to perform diverse tasks, such as sensorless adaptive optics in optically complex specimens (Fig. 1c). We believe this flexibility is necessary for the software to accommodate the diverse modalities of LSFM and to integrate feedback mechanisms.

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Fig. 1: Navigate provides a GUI with access to reconfigurable smart acquisition pipelines and runs on multiple types of light-sheet configurations.

Data availability

Imaging data presented in figures are available upon request.

Code availability

The source code for navigate is available on GitHub (https://github.com/TheDeanLab/navigate) and PyPI (https://pypi.org/project/navigate-micro/). Queries and feedback can be provided by creating an issue on GitHub. Documentation on how to extend navigate is provided in the Supplementary Documentation (and is kept up to date at https://thedeanlab.github.io/navigate/). A plug-in template is available at https://github.com/TheDeanLab/navigate-plugin-template.

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Acknowledgements

The authors wish to thank G. Danuser and F. Zhou for discussions about software design, A. York and N. Thayer for their open-source concurrency toolkit, and E. Wylie, S. Rapuri, R. Gupta and S. Mamtani for their contributions to the graphical user interface. This work was funded by the NIH National Institute of General Medical Science (RM1GM145399 to K.M.D., R35GM133522 to R.F.), the NIH National Cancer Institute (U54CA268072 to K.M.D. and R.F., R01CA238519 to S.D.C.) and the Cancer Prevention Research Institute of Texas (RR1900371 to S.D.C.).

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Author notes

  1. These authors contributed equally: Zach Marin, Xiaoding Wang.

Authors and Affiliations

  1. Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA

    Zach Marin, Xiaoding Wang, Dax W. Collison, Conor McFadden, Jinlong Lin, Hazel M. Borges, Bingying Chen, Dushyant Mehra, Qionghua Shen, Seweryn Gałecki, Stephan Daetwyler, Reto Fiolka & Kevin M. Dean

  2. Max Perutz Labs, Department of Structural and Computational Biology, University of Vienna, Vienna, Austria

    Zach Marin

  3. Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland

    Seweryn Gałecki

  4. Center for Biological Physics and Department of Physics, Arizona State University, Tempe, AZ, USA

    Steven J. Sheppard, Phu Thien & Douglas P. Shepherd

  5. Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA

    Baylee A. Porter & Suzanne D. Conzen

  6. Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX, USA

    Kevin M. Dean

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Contributions

Z.M., X.W., D.W.C. and K.M.D. designed the software. Z.M., X.W., D.W.C., B.C., C.M., D.M., S.D., S.J.S., P.T., D.P.S. and K.M.D. wrote the code. Z.M., J.L., B.C., C.M., H.M.B. and K.M.D. tested the software. Q.S., H.M.B., S.G., B.A.P. and S.D.C. provided biological samples. C.M. and R.F. implemented adaptive optics routines. K.M.D. supervised the design and development of software, microscopes and tissue preparation methods. Z.M., X.W. and K.M.D. wrote the manuscript. All authors discussed the project and edited the manuscript.

Corresponding author

Correspondence to Kevin M. Dean.

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Competing interests

K.M.D. and R.F. have a patent covering ASLM (US10989661) and consultancy agreements with 3i, Inc (Denver, CO, USA). K.M.D has an ownership interest in Discovery Imaging Systems, LLC. The remaining authors declare no competing interests.

Peer review

Peer review information

Nature Methods thanks Adam Glaser, Kurt Weiss, and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Supplementary information

Supplementary Information

Supplementary Figures 1 and 2, Table 1 and User Guide

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Marin, Z., Wang, X., Collison, D.W. et al. Navigate: an open-source platform for smart light-sheet microscopy. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02413-4

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