ArticleNature methods2024
Image processing tools for petabyte-scale light sheet microscopy data.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- CALIPERS: Cell cycle-aware live imaging for phenotyping experiments and regeneration studies.Nature communications · 2026Article
- GloBIAS: strengthening the foundations of bioimage analysis.Nature methods · 2026Article
- Challenges of microscopy technology dissemination to resource-constrained communities.Nature methods · 2026Article
- A physics-informed alternative to Richardson-Lucy deconvolution across SNR regimes without iteration cutoffs.Nature communications · 2026Article
- A multimodal adaptive optical microscope for in vivo imaging from molecules to organisms.Nature methods · 2026Article
- Polarization-engineered aberration-resilient light sheet microscopy.bioRxiv : the preprint server for biology · 2026Article
- Enhancer placement impacts transcriptional dynamics in Drosophila embryos.Nature communications · 2026Article
- A single cluster of RNA Polymerase II molecules is stably associated with active genes.Nature communications · 2026Article
- Article
- A modular tissue-clearing framework integrated with light-field microscopy enables rapid volumetric phenotyping of cardiac tissue.Research square · 2026Article
- A Pandemic-Scale Ancestral Recombination Graph for SARS-CoV-2.bioRxiv : the preprint server for biology · 2025Article
- Altair-LSFM A High-Resolution, Easy-to-Build Light-Sheet Microscope for Sub-Cellular Imaging.bioRxiv : the preprint server for biology · 2025Article
- CELLECT: contrastive embedding learning for large-scale efficient cell tracking.Nature methods · 2025Article
- Mesoscale volumetric fluorescence imaging at nanoscale resolution by photochemical sectioning.Science (New York, N.Y.) · 2025Article
- HCS-3DX, a next-generation AI-driven automated 3D-oid high-content screening system.Nature communications · 2025Article
- Multi-immersion Oblique Plane Microscope (miOPM): A reconfigurable platform for high-resolution Light-Sheet Fluorescence Microscopy.bioRxiv : the preprint server for biology · 2025Article
- Content-aware foveated camera for multi-target tracking.Optics express · 2025Article
- Fourier-based three-dimensional multistage transformer for aberration correction in multicellular specimens.Nature methods · 2025Article
- A single cluster of RNA Polymerase II molecules is stably associated with active genes.bioRxiv : the preprint server for biology · 2025Article
- Feature-driven whole-tissue imaging with subcellular resolution.Cell reports methods · 2025Article
Corrections and comments
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Authors and funding
16 authors.
Funding
Abstract
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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