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2 Publications

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    Betzig Lab
    08/07/24 | A Cell Observatory to reveal the subcellular foundations of life.
    Betzig E
    Nat Methods. 2024 Aug 07:. doi: 10.1038/s41592-024-02379-3

    Imaging the 4D choreography of subcellular events in living multicellular organisms at high spatiotemporal resolution could reveal life’s fundamental principles. Yet extracting these principles from petabyte-scale image data requires fusing advanced light microscopy and cutting-edge machine learning models with biological insight and expertise.

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    Betzig Lab
    10/17/24 | Image processing tools for petabyte-scale light sheet microscopy data.
    Xiongtao Ruan , Matthew Mueller , Gaoxiang Liu , Frederik Görlitz , Tian-Ming Fu , Daniel E. Milkie , Joshua Lillvis , Alison Killilea , Eric Betzig , Srigokul Upadhyayula
    Nat. Methods. 2024 Oct 17:. doi: 10.1038/s41592-024-02475-4

    Light sheet microscopy is a powerful technique for high-speed three-dimensional imaging of subcellular dynamics and large biological specimens. However, it often generates datasets ranging from hundreds of gigabytes to petabytes in size for a single experiment. Conventional computational tools process such images far slower than the time to acquire them and often fail outright due to memory limitations. To address these challenges, we present PetaKit5D, a scalable software solution for efficient petabyte-scale light sheet image processing. This software incorporates a suite of commonly used processing tools that are optimized for memory and performance. Notable advancements include rapid image readers and writers, fast and memory-efficient geometric transformations, high-performance Richardson-Lucy deconvolution and scalable Zarr-based stitching. These features outperform state-of-the-art methods by over one order of magnitude, enabling the processing of petabyte-scale image data at the full teravoxel rates of modern imaging cameras. The software opens new avenues for biological discoveries through large-scale imaging experiments.

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