ArticleNature protocols2019
Advanced CUBIC tissue clearing for whole-organ cell profiling.
Article in Nature protocols, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 152 papers.
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Who cites it
152 citing papers in PubMed.
- Article
- Most Early-Born Subplate Neurons Persist as Layer 6b Neurons in the Adult Mouse Neocortex.The Journal of comparative neurology · 2026Article
- A scale CUBIC-based clearing protocol preserves fluorescence in mouse rib bone and cartilage.JBMR plus · 2026Article
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Whole-organ single-cell mapping defines growth dynamics and clonal organization in developing and adult zebrafish livers.PLoS biology · 2026Article
- Article
- Deep-learning triage of three-dimensional pathology datasets for comprehensive and efficient pathologist assessments.Nature biomedical engineering · 2026Article
- Article
- Article
- Three-Dimensional Architecture of Ectopic Epithelium and Vasculature in Ovarian Endometriosis Revealed by Tissue-Clearing Imaging.Cell proliferation · 2026Article
- Scanning Bessel beam microscopy with a protected and corrective objective for solvent-cleared large samples.iScience · 2026Article
- Ectomesenchyme contributes to epidermal stem cell formation through mesenchymal-to-epithelial transition.Nature communications · 2026Article
- A uniform tissue-clearing framework and mesoSPIM-ultra enable cm-scale single-neuron tracing.bioRxiv : the preprint server for biology · 2026Article
- Article
- Size-Modulated Mesoderm-Endoderm Divergence and Myocardial Cavitation in Micropatterned Cardioids.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Frequency-dependent cerebellar circuits independently gate social vocalizations and movement.bioRxiv : the preprint server for biology · 2026Article
- 3D imaging with enhanced transparency, signal-to-background ratios, and antigen detection using HyPer-3D.Cell reports methods · 2026Article
- A spatially localised cryoinjury protocol to study liver regeneration in zebrafish.STAR protocols · 2026Article
- ClearScope: A Fully Integrated Light-Sheet Theta Microscope for Sub-Micron-Resolution Imaging Without Lateral Size Constraints.Journal of imaging · 2026Article
- Article
92 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tissue-clearing techniques are powerful tools for biological research and pathological diagnosis. Here, we describe advanced clear, unobstructed brain imaging cocktails and computational analysis (CUBIC) procedures that can be applied to biomedical research. This protocol enables preparation of high-transparency organs that retain fluorescent protein signals within 7-21 d by immersion in CUBIC reagents. A transparent mouse organ can then be imaged by a high-speed imaging system (>0.5 TB/h/color). In addition, to improve the understanding and simplify handling of the data, the positions of all detected cells in an organ (3-12 GB) can be extracted from a large image dataset (2.5-14 TB) within 3-12 h. As an example of how the protocol can be used, we counted the number of cells in an adult whole mouse brain and other distinct anatomical regions and determined the number of cells transduced with mCherry following whole-brain infection with adeno-associated virus (AAV)-PHP.eB. The improved throughput offered by this protocol allows analysis of numerous samples (e.g., >100 mouse brains per study), providing a platform for next-generation biomedical research.
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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.