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inTRACKtive: a web-based tool for interactive cell tracking visualization

Nature Methods (2025)Cite this article

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The field of developmental biology is undergoing a profound transformation, driven by groundbreaking advances across multiple disciplines. Light-sheet microscopy enables rapid, large-scale, multicolor imaging of developing embryos in unprecedented detail, allowing scientists to capture dynamic processes as they unfold in real time1,2,3. Simultaneously, the advent of advanced cell tracking technologies, such as Ultrack4, Linajea5, Elephant, TGMM6, Trackmate, Mastodon and TrackAstra, has made it possible to follow individual cells throughout embryonic development with remarkable precision and speed. These innovations, which have emerged in the past two decades, are only now realizing their full potential for embryology. This unprecedented level of detail opens the door to answering fundamental questions about tissue development, organ formation and the intricate orchestration of the cell behaviors that govern the entire embryo7.

While these imaging datasets hold the potential for biological insights, accessing and interacting with such complex data typically demands highly specialized technical expertise and substantial computational resources. Existing software tools allow visualization and analysis of cell tracking data (for example, napari8, TrackMate’s TrackScheme, Mastodon and CellTracksColab), However, while powerful in their respective application domains, most of these approaches require native software, have limited 3D support, or are intended for the curation of tracks, not the interactive exploration of large cell tracking datasets. Consequently, only a limited subset of researchers can fully leverage these data, creating a barrier to broader adoption.

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Fig. 1: inTRACKtive cell tracking viewer and its applications.

Data availability

The tracking data presented in this study are available for download from the Virtual Embryo Zoo website (https://embryozoo.org). The datasets are either sourced from the original authors or tracked by us using the Ultrack4 algorithm (Supplementary Table 1). All data have been converted and normalized to a common format (Supplementary Fig. 3) compatible with inTRACKtive and napari, ensuring seamless interaction and visualization.

Code availability

The repository for inTRACKtive, including documentation, example code and videos, can be found at https://github.com/royerlab/inTRACKtive.

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Acknowledgements

We extend our gratitude to all the original authors who kindly provided data and guidance: P. Keller, H. Shroff, K. McDole, A. Jain, R. Haase and G. Malandain. We thank the Royer group at CZ Biohub SF and E. Gomez-de-Mariscal for feedback on inTRACKtive and the Virtual Embryo Zoo website. We appreciate S. Schmid’s constructive feedback on the manuscript. We thank CZI for the Science Design System (SDS) UI component library. Chan Zuckerberg Biohub San Francisco (CZB SF) funded this work. We thank CZB SF donors P. Chan and M. Zuckerberg for their generous support.

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Authors and Affiliations

  1. Chan Zuckerberg Biohub, San Francisco, CA, USA

    Teun A. P. M. Huijben, Kyle Awayan, Jordão Bragantini, Merlin Lange & Loïc A. Royer

  2. Chan Zuckerberg Initiative, Redwood City, CA, USA

    Ashley G. Anderson III, Andrew Sweet, Erin Hoops, Connor Larsen & Chi-Li Chiu

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  1. Teun A. P. M. Huijben
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  2. Ashley G. Anderson III
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  10. Loïc A. Royer
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Contributions

J.B. and L.A.R. conceived the research. A.A., A.S., E.H., C.L. and C.-L.C. developed the initial version of inTRACKtive. T.A.P.M.H. collected the light-sheet datasets from the original authors, converted them into the applicable formats, and further developed inTRACKtive (guided by A.A. and A.S.). K.A. and T.A.P.M.H. built the Virtual Embryo Zoo website. J.B. performed tracking of the Tribolium and zebrafish data using Ultrack. M.L. provided insight into the zebrafish tailbud migration. T.A.P.M.H. and L.A.R. wrote the paper. T.A.P.M.H. led the project. L.A.R. supervised the research. All authors contributed to editing the manuscript.

Corresponding authors

Correspondence to Teun A. P. M. Huijben or Loïc A. Royer.

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Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Methods thanks Juhyun Lee, John Murray, and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Supplementary information

Supplementary Information

Supplementary Methods, Table 1 and Figs. 1–3

Supplementary Video 1

Overview of the inTRACKtive web viewer

Supplementary Video 2

Overview of the Virtual Embryo Zoo

Supplementary Video 3

Coloring cells by attribute

Supplementary Video 4

Visualizing velocity, density and structure tensor

Supplementary Video 5

How to visualize your own data: using inTRACKtive from the command line, from napari, from a Jupyter notebook, and within a Jupyter notebook

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Huijben, T.A.P.M., Anderson, A.G., Sweet, A. et al. inTRACKtive: a web-based tool for interactive cell tracking visualization. Nat Methods (2025). https://doi.org/10.1038/s41592-025-02777-1

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