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Related Concept Videos

Brain Imaging01:14

Brain Imaging

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Brain imaging technologies provide critical insights into both the structure and function of the human brain, enabling medical professionals and researchers to diagnose, study, and treat neurological disorders or psychiatric disorders more effectively.
These technologies include computerized axial tomography (CAT or CT scans), positron-emission tomography (PET scans),  magnetic resonance imaging (MRI),  functional magnetic resonance imaging (fMRI), and Transcranial Magnetic...
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Related Experiment Video

Updated: Jan 11, 2026

3D Scanning Technology Bridging Microcircuits and Macroscale Brain Images in 3D Novel Embedding Overlapping Protocol
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scBrainScope: cross-species multidimensional brain atlas.

Siying Qin1, Yuexi Yang1, Haoyu Wang1

  • 1State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, Jiangsu, China.

Nucleic Acids Research
|November 17, 2025
PubMed
Summary
This summary is machine-generated.

scBrainScope is a new interactive brain atlas integrating single-cell and spatial transcriptomic data across species and conditions. This resource aids exploration of brain cell identity, gene programs, and organization for neuroscience research.

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Area of Science:

  • Neuroscience
  • Genomics
  • Bioinformatics

Background:

  • The brain's complexity necessitates integrated data resources.
  • Existing brain atlases lack comprehensive gene expression and analysis tools.
  • Understanding brain evolution, development, and disease requires multi-dimensional data integration.

Purpose of the Study:

  • To develop scBrainScope, an interactive transcriptomic atlas of the brain.
  • To integrate diverse brain datasets, including single-cell, bulk RNA, and spatial sequencing data.
  • To provide analytical tools for exploring brain features across species, regions, developmental stages, and diseases.

Main Methods:

  • Compiled single-cell sequencing data from 135 species (433 brain regions, 198 developmental stages, 100 diseases).
  • Integrated 737 bulk RNA sequencing datasets and 1154 spatial datasets.
  • Developed six atlas modules (AtlasScope, RegionScope, TissueScope, SpaceScope, PathoScope, AgeScope) and three analytical modules (sPandora, ePandora, cPandora).

Main Results:

  • Created a comprehensive, interactive transcriptomic atlas of the brain.
  • Enabled multi-scale and multi-dimensional investigation of cell identity, gene programs, and spatial organization.
  • Facilitated comparative analysis across diverse species, developmental stages, and neurological conditions.

Conclusions:

  • scBrainScope offers a valuable, data-rich resource for neuroscience, evolutionary biology, and translational medicine.
  • The platform supports in-depth exploration of brain transcriptomics.
  • Provides a foundation for future discoveries in brain research and disease understanding.