ArticleNature methods2021
Universal autofocus for quantitative volumetric microscopy of whole mouse brains.
Article in Nature methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 73 citations in OpenAlex.
- Quantitative evaluation of LED-based optical autofocus module.Journal of microscopy · 2026Article
- A coma pattern-based autofocusing method resolves bacterial cold shock response at single-cell level.eLife · 2026Article
- Testosterone protects from metabolic syndrome-associated lung dysfunction in a high-fat diet rabbit model.Endocrinology · 2026Article
- Digital defocus aberration interference for automated optical microscopy.Nature communications · 2026Article
- CellPheno: A High-throughput Computational Platform for Quantifying Cellular Resolution Whole Brain Microscopy Images.bioRxiv : the preprint server for biology · 2026Article
- Mechanical de-skewing enables high-resolution imaging of thin tissue slices with a mesoSPIM light-sheet microscope.Biomedical optics express · 2026Article
- Illuminating Satellite Cells: Light Sheet Fluorescence Microscopy for 3D Imaging of Murine Skeletal Muscles Damaged by Ex Vivo Forced Eccentric Contraction.Microscopy research and technique · 2025Article
- Myelinated fiber labeling and orientation mapping of the human brain with light-sheet fluorescence microscopy.NeuroImage · 2025Article
- Quantitative cytoarchitectural phenotyping of deparaffinized human brain tissues.Communications biology · 2025Article
- Unlocking the potential of large-scale 3D imaging with tissue clearing techniques.Microscopy (Oxford, England) · 2025Review
- Open-source 3D active sample stabilization for fluorescence microscopy.Biophysical reports · 2025Article
- Microscopy with microfluidics in microgravity using FlightScope.NPJ microgravity · 2025Article
- A multiwell plate approach to increase the sample throughput during tissue clearing.Nature protocols · 2025Review
- Active remote focus stabilization in oblique plane microscopy.Biomedical optics express · 2025Article
- Brain-wide immunolabeling and tissue clearing applications for engram research.Neurobiology of learning and memory · 2025Review
- Precision autofocus in optical microscopy with liquid lenses controlled by deep reinforcement learning.Microsystems & nanoengineering · 2024Article
- Active Remote Focus Stabilization in Oblique Plane Microscopy.bioRxiv : the preprint server for biology · 2024Article
- Deep 3D histology powered by tissue clearing, omics and AI.Nature methods · 2024Review
- Robust autofocus method based on patterned active illumination and image cross-correlation analysis.Biomedical optics express · 2024Article
- Trackoscope: A low-cost, open, autonomous tracking microscope for long-term observations of microscale organisms.PloS one · 2024Article
Corrections and comments
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Authors and funding
13 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Unbiased quantitative analysis of macroscopic biological samples demands fast imaging systems capable of maintaining high resolution across large volumes. Here we introduce RAPID (rapid autofocusing via pupil-split image phase detection), a real-time autofocus method applicable in every widefield-based microscope. RAPID-enabled light-sheet microscopy reliably reconstructs intact, cleared mouse brains with subcellular resolution, and allowed us to characterize the three-dimensional (3D) spatial clustering of somatostatin-positive neurons in the whole encephalon, including densely labeled areas. Furthermore, it enabled 3D morphological analysis of microglia across the entire brain. Beyond light-sheet microscopy, we demonstrate that RAPID maintains high image quality in various settings, from in vivo fluorescence imaging to 3D tracking of fast-moving organisms. RAPID thus provides a flexible autofocus solution that is suitable for traditional automated microscopy tasks as well as for quantitative analysis of large biological specimens.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.