Image processing tools for petabyte-scale light sheet microscopy data
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.
Authors
- Frederik Görlitz (ORCID: https://orcid.org/0000-0002-8415-1820)
- Marc Nienhaus
- Tian-Ming Fu (ORCID: https://orcid.org/0000-0001-6265-0859)
- Srigokul Upadhyayula (ORCID: https://orcid.org/0000-0001-6727-5883)
- Matthew Mueller (ORCID: https://orcid.org/0000-0003-0774-1031)
- Wilmene Hercule
- Jason Li Hong
- Xiongtao Ruan (ORCID: https://orcid.org/0000-0001-5322-3249)
- Eric Betzig (ORCID: https://orcid.org/0000-0002-4192-1274)
- Alison N. Killilea (ORCID: https://orcid.org/0000-0002-8308-8196)
- Gaoxiang Liu (ORCID: https://orcid.org/0000-0002-1001-0064)
- Joshua L. Lillvis (ORCID: https://orcid.org/0000-0002-6235-8759)
- Daniel E. Milkie (ORCID: https://orcid.org/0000-0002-3917-6965)
- Johnny Gan Chong (ORCID: https://orcid.org/0000-0001-8925-6368)
- Alexander Kühn
- Chu Yi Aaron Herr
Institutions
- Howard Hughes Medical Institute (US)
- Lawrence Berkeley National Laboratory (US)
- University of Freiburg (DE)
- Janelia Research Campus (US)
- Princeton University (US)
- Chan Zuckerberg Initiative (United States) (US)
- University of California, Berkeley (US)
Publication Details
- Journal
- Nature Methods
- Published
- 2024-10-17
- DOI
- https://doi.org/10.1038/s41592-024-02475-4
- Citations
- 35
- Primary Topic
- Advanced Fluorescence Microscopy Techniques
- Type
- article
- Field-Weighted Citation Impact
- 23.18
Funders
- Howard Hughes Medical Institute
- U.S. Department of Energy
- California Institute for Regenerative Medicine
- Nvidia
- National Energy Research Scientific Computing Center
- Office of Science
- Laboratory Directed Research and Development
- Lawrence Berkeley National Laboratory