ArticleCell reports methods2021
CUBIC-Cloud provides an integrative computational framework toward community-driven whole-mouse-brain mapping.
Article in Cell reports methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 26 citations in OpenAlex.
- 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
- Brain-wide input-output analysis of tuberal nucleus somatostatin neurons reveals hierarchical circuits for orchestrating feeding behavior.Nature communications · 2025Article
- Unlocking the potential of large-scale 3D imaging with tissue clearing techniques.Microscopy (Oxford, England) · 2025Review
- An extended and improved CCFv3 annotation and Nissl atlas of the entire mouse brain.Imaging neuroscience (Cambridge, Mass.) · 2025Article
- Cortical parvalbumin neurons are responsible for homeostatic sleep rebound through CaMKII activation.Nature communications · 2024Article
- Realization of cellomics to dive into the whole-body or whole-organ cell cloud.Nature methods · 2024Article
- descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques.Nature communications · 2024Article
- A novel tauopathy model mimicking molecular and spatial aspects of human tau pathology.Brain communications · 2024Article
- Tissue clearing method in visualization of cancer progression and metastasis.Upsala journal of medical sciences · 2024Review
- Waxholm Space atlas of the rat brain: a 3D atlas supporting data analysis and integration.Nature methods · 2023Article
- Whole-mouse clearing and imaging at the cellular level with vDISCO.Nature protocols · 2023Review
- Visualization of Organ-Specific Lymphatic Growth: An Efficient Approach to Labeling Molecular Markers in Cleared Tissues.International journal of molecular sciences · 2023Article
- Article
- Review
- An analysis modality for vascular structures combining tissue-clearing technology and topological data analysis.Nature communications · 2022Article
- Mesoscale microscopy and image analysis tools for understanding the brain.Progress in biophysics and molecular biology · 2022Review
- Digital Brain Maps and Virtual Neuroscience: An Emerging Role for Light-Sheet Fluorescence Microscopy in Drug Development.Frontiers in neuroscience · 2022Review
- Towards organism-level systems biology by next-generation genetics and whole-organ cell profiling.Biophysical reviews · 2021Review
- Emerging imaging methods to study whole-brain function in rodent models.Translational psychiatry · 2021Review
- TISSUE CLEARING.Nature reviews. Methods primers · 2021Article
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advancements in tissue clearing technologies have offered unparalleled opportunities for researchers to explore the whole mouse brain at cellular resolution. With the expansion of this experimental technique, however, a scalable and easy-to-use computational tool is in demand to effectively analyze and integrate whole-brain mapping datasets. To that end, here we present CUBIC-Cloud, a cloud-based framework to quantify, visualize, and integrate mouse brain data. CUBIC-Cloud is a fully automated system where users can upload their whole-brain data, run analyses, and publish the results. We demonstrate the generality of CUBIC-Cloud by a variety of applications. First, we investigated the brain-wide distribution of five cell types. Second, we quantified Aβ plaque deposition in Alzheimer's disease model mouse brains. Third, we reconstructed a neuronal activity profile under LPS-induced inflammation by c-Fos immunostaining. Last, we show brain-wide connectivity mapping by pseudotyped rabies virus. Together, CUBIC-Cloud provides an integrative platform to advance scalable and collaborative whole-brain mapping.
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