Image processing tools for petabyte-scale light sheet microscopy data Article Swipe
Xiongtao Ruan
,
Matthew Mueller
,
Gaoxiang Liu
,
Frederik Görlitz
,
Tian-Ming Fu
,
Daniel E. Milkie
,
Joshua L. Lillvis
,
Alexander Kühn
,
Johnny Gan Chong
,
Jason Li Hong
,
Chu Yi Aaron Herr
,
Wilmene Hercule
,
Marc Nienhaus
,
Alison N. Killilea
,
Eric Betzig
,
Srigokul Upadhyayula
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1038/s41592-024-02475-4
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/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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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1038/s41592-024-02475-4
- OA Status
- hybrid
- Cited By
- 29
- References
- 71
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4403491578
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W4403491578Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1038/s41592-024-02475-4Digital Object Identifier
- Title
-
Image processing tools for petabyte-scale light sheet microscopy dataWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-10-17Full publication date if available
- Authors
-
Xiongtao Ruan, Matthew Mueller, Gaoxiang Liu, Frederik Görlitz, Tian-Ming Fu, Daniel E. Milkie, Joshua L. Lillvis, Alexander Kühn, Johnny Gan Chong, Jason Li Hong, Chu Yi Aaron Herr, Wilmene Hercule, Marc Nienhaus, Alison N. Killilea, Eric Betzig, Srigokul UpadhyayulaList of authors in order
- Landing page
-
https://doi.org/10.1038/s41592-024-02475-4Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
hybridOpen access status per OpenAlex
- OA URL
-
https://doi.org/10.1038/s41592-024-02475-4Direct OA link when available
- Concepts
-
Petabyte, Microscopy, Scale (ratio), Light sheet fluorescence microscopy, Computer science, Image processing, Nanotechnology, Computer graphics (images), Materials science, Biology, Computer vision, Image (mathematics), Data mining, Big data, Optics, Physics, Scanning confocal electron microscopy, Quantum mechanicsTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
29Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 23, 2024: 6Per-year citation counts (last 5 years)
- References (count)
-
71Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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