Dataset Information

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas.

ABSTRACT: Recent large-scale collaborations are generating major surveys of cell types and connections in the mouse brain, collecting large amounts of data across modalities, spatial scales, and brain areas. Successful integration of these data requires a standard 3D reference atlas. Here, we present the Allen Mouse Brain Common Coordinate Framework (CCFv3) as such a resource. We constructed an average template brain at 10 μm voxel resolution by interpolating high resolution in-plane serial two-photon tomography images with 100 μm z-sampling from 1,675 young adult C57BL/6J mice. Then, using multimodal reference data, we parcellated the entire brain directly in 3D, labeling every voxel with a brain structure spanning 43 isocortical areas and their layers, 329 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures. CCFv3 can be used to analyze, visualize, and integrate multimodal and multiscale datasets in 3D and is openly accessible (https://atlas.brain-map.org/).

SUBMITTER: Wang Q

PROVIDER: S-EPMC8152789 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Publications

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas.

Wang Quanxin Q Ding Song-Lin SL Li Yang Y Royall Josh J Feng David D Lesnar Phil P Graddis Nile N Naeemi Maitham M Facer Benjamin B Ho Anh A Dolbeare Tim T Blanchard Brandon B Dee Nick N Wakeman Wayne W Hirokawa Karla E KE Szafer Aaron A Sunkin Susan M SM Oh Seung Wook SW Bernard Amy A Phillips John W JW Hawrylycz Michael M Koch Christof C Zeng Hongkui H Harris Julie A JA Ng Lydia L

Cell 20200507 4

Recent large-scale collaborations are generating major surveys of cell types and connections in the mouse brain, collecting large amounts of data across modalities, spatial scales, and brain areas. Successful integration of these data requires a standard 3D reference atlas. Here, we present the Allen Mouse Brain Common Coordinate Framework (CCFv3) as such a resource. We constructed an average template brain at 10 μm voxel resolution by interpolating high resolution in-plane serial two-photon tom ...[more]

PMID: 32386544

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Project description:The human brain is a complex interconnected structure controlling all elementary and high-level cognitive tasks. It is composed of many regions that exhibit specific distributions of cell types and distinct patterns of functional connections. This complexity is rooted in differential transcription. The constituent cell types of different brain regions express distinctive combinations of genes as they develop and mature, ultimately shaping their functional state in adulthood. How precisely the genetic information of anatomical structures is connected to their underlying biological functions remains an open question in modern neuroscience. A major challenge is the identification of "universal patterns", which do not depend on the particular individual, but are instead basic structural properties shared by all brains. Despite the vast amount of gene expression data available at both the bulk and single-cell levels, this task remains challenging, mainly due to the lack of suitable data mining tools. In this paper, we propose an approach to address this issue based on a hierarchical version of Stochastic Block Modeling. Thanks to its specific choice of priors, the method is particularly effective in identifying these universal features. We use as a laboratory to test our algorithm a dataset obtained from six independent human brains from the Allen Human Brain Atlas. We show that the proposed method is indeed able to identify universal patterns much better than more traditional algorithms such as Latent Dirichlet Allocation or Weighted Correlation Network Analysis. The probabilistic association between genes and samples that we find well represents the known anatomical and functional brain organization. Moreover, leveraging the peculiar "fuzzy" structure of the gene sets obtained with our method, we identify examples of transcriptional and post-transcriptional pathways associated with specific brain regions, highlighting the potential of our approach.

Dataset Information

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas.

Publications

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas.

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