Mouse Brain Atlas

Adult mouse primary visual cortex

openproblems_v1

Info

openproblems_v1/allen_brain_atlas
Tasic et al. (2016)
1.91 GiB
02-02-2024
14249 cells × 34617 genes

Used in

Description

A murine brain atlas with adjacent cell types as assumed benchmark truth, inferred from deconvolution proportion correlations using matching 10x Visium slides (see Dimitrov et al., 2022).

Preview

dataset is an AnnData object with n_obs × n_vars = 14249 × 34617 with slots:

Reference

Name Description Type Data type Size
obs
cell_type Classification of the cell type based on its characteristics and function within the tissue or organism. vector category 14249
size_factors The size factors created by the normalisation method, if any. vector float32 14249
var
feature_name A human-readable name for the feature, usually a gene symbol. vector object 34617
hvg Whether or not the feature is considered to be a ‘highly variable gene’ vector bool 34617
hvg_score A ranking of the features by hvg. vector float64 34617
obsp
knn_connectivities K nearest neighbors connectivities matrix. sparsematrix float32 14249 × 14249
knn_distances K nearest neighbors distance matrix. sparsematrix float64 14249 × 14249
obsm
X_pca The resulting PCA embedding. densematrix float32 14249 × 50
varm
pca_loadings The PCA loadings matrix. densematrix float64 34617 × 50
layers
counts Raw counts sparsematrix float32 14249 × 34617
normalized Normalised expression values sparsematrix float32 14249 × 34617
uns
dataset_description Long description of the dataset. atomic str 1
dataset_id A unique identifier for the dataset. This is different from the obs.dataset_id field, which is the identifier for the dataset from which the cell data is derived. atomic str 1
dataset_name A human-readable name for the dataset. atomic str 1
dataset_organism The organism of the sample in the dataset. atomic str 1
dataset_reference Bibtex reference of the paper in which the dataset was published. atomic str 1
dataset_summary Short description of the dataset. atomic str 1
dataset_url Link to the original source of the dataset. atomic str 1
knn Supplementary K nearest neighbors data. dict 3
normalization_id Which normalization was used atomic str 1
pca_variance The PCA variance objects. dict 2

References

Tasic, Bosiljka, Vilas Menon, Thuc Nghi Nguyen, Tae Kyung Kim, Tim Jarsky, Zizhen Yao, Boaz Levi, et al. 2016. “Adult Mouse Cortical Cell Taxonomy Revealed by Single Cell Transcriptomics.” Nature Neuroscience 19 (2): 335–46. https://doi.org/10.1038/nn.4216.