ArticleNature neuroscience2018
A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing.
Article in Nature neuroscience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 169 papers.
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Who cites it
169 citing papers in PubMed, 305 citations in OpenAlex.
- Thrombin-dependent nanoscale architecture and fibrinolytic remodeling of hydrated fibrin clots revealed by expansion microscopy.Journal of thrombosis and haemostasis : JTH · 2026Article
- Barcoded Rabies In Situ Connectomics for high-throughput reconstruction of neural circuits.Nature communications · 2026Article
- In vivo tissue clearing with tartrazine and other dye molecules.Communications biology · 2026Review
- Engineering Brain Injury In Vitro: Human iPSC-Based Organoids in Microfluidic Systems.Applied sciences (Basel, Switzerland) · 2026Article
- Article
- Achieving transient and reversible optical transparency in live mice with tartrazine.Nature protocols · 2026Review
- A mouse brain atlas based on dendritic microenvironments.Nature neuroscience · 2026Article
- Innovative Technologies for Kidney Research: Three-Dimensional Imaging and Quantification.Seminars in nephrology · 2026Review
- MeCP2 regulates telencephalic development in human cerebral organoids.Cell reports · 2025Article
- Investigating urea is an ideal additive to the Accu-OptiClearing delipidation cocktail.Scientific reports · 2025Article
- Uniform volumetric single-cell processing for organ-scale molecular phenotyping.Nature biotechnology · 2025Article
- Rapid and Solvent-Free, 2-hydroxyethyl Methacrylate (HEMA)-Acrylamide (AAm) Copolymer-Based Optical Clearing of Tissue for Fluorescent Imaging.Bio-protocol · 2025Article
- Molecularly defined cellular atlas of the entire mouse brain with isotropic single-cell resolution.Nature communications · 2025Article
- Single-cell synaptome mapping of endogenous protein subpopulations in mammalian brain.Nature communications · 2025Article
- Molecular profiling of brain endothelial cell to astrocyte endfoot communication in mouse and human.Nature communications · 2025Article
- A framework to determine active neurons and networks within the mouse brain reveals how brain activity changes over the course of the day.PLoS biology · 2025Article
- Color-neutral and reversible tissue transparency enables longitudinal deep-tissue imaging in live mice.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- SeeThrough: a rationally designed skull clearing technique for in vivo brain imaging.Nature communications · 2025Article
- Advances in tissue optical clearing for 3D imaging in large animal.Frontiers of optoelectronics · 2025Review
- Neuroprotective liver portal area macrophages attenuate hepatic inflammation.Nature immunology · 2025Article
109 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
14 authors at 8 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A three-dimensional single-cell-resolution mammalian brain atlas will accelerate systems-level identification and analysis of cellular circuits underlying various brain functions. However, its construction requires efficient subcellular-resolution imaging throughout the entire brain. To address this challenge, we developed a fluorescent-protein-compatible, whole-organ clearing and homogeneous expansion protocol based on an aqueous chemical solution (CUBIC-X). The expanded, well-cleared brain enabled us to construct a point-based mouse brain atlas with single-cell annotation (CUBIC-Atlas). CUBIC-Atlas reflects inhomogeneous whole-brain development, revealing a significant decrease in the cerebral visual and somatosensory cortical areas during postnatal development. Probabilistic activity mapping of pharmacologically stimulated Arc-dVenus reporter mouse brains onto CUBIC-Atlas revealed the existence of distinct functional structures in the hippocampal dentate gyrus. CUBIC-Atlas is shareable by an open-source web-based viewer, providing a new platform for whole-brain cell profiling.
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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.