Brain | nibuiroフラグメント β

Allen Brain Atlas

Mouse

3-dimensional atlas

http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2017/
ここに.objデータ, 各パーツの座標データであるstructure_centers.csvがあります. annotation_XX.nrrdファイルはこれらがパッケージ化されたものです.
[https://qiita.com/tatsunidas/items/32d3d0b362b0864b8579](NRRDファイルの読み込み – Qiita)

Ontology (as a hierarchically structured json file)

http://api.brain-map.org/api/v2/structure_graph_download/1.json

Transcriptional profiling: RNA-Seq Data

File Size Type Description

Readme

12 KB .txt
Read-me file with additional information about the other files in this directory
Table of cell metadata 835 KB .csv
Metadata about each cell. Each entry has an _order, _label, and _color column.
Gene expression matrix 5.6 GB .tome
Gene expression matrices provided as an HDF5 file with column-indexed sparse matrices. Exon and intron counts are stored separately. 
See “readme.txt” for data access instructions.
Taxonomy of clusters 44 KB .json
Serialized cluster hierarchy with all node information embedded.
Probability matrix of cluster membership 690KB .csv
Probability matrix that each cell will be in each cell type.
Taxonomy information 1 KB .txt
Metadata about the taxonomy.
Gene Expression by Cluster, median 19 MB .csv
Gene expression aggregated per cluster, calculated as medians.
2D coordinates 1.5 MB .csv
TSNE coordinates for each cell, as shown in the Transcriptomics Explorer

Human

3-dimensional atlas

http://download.alleninstitute.org/informatics-archive/allen_human_reference_atlas_3d_2020/version_1/
ここにannotation.nii.gz(NIfTIイメージ)があります.
MATLABなどですぐに見ることが出来ますが, volshow関数は2019aからの機能となります.

Ontology

  • Download the “Human Brain Atlas” ontology as a CSV file
    http://api.brain-map.org/api/v2/data/query.csv?criteria=model::Structure,
    rma::criteria,[ontology_id$eq7],
    rma::options[order$eq%27structures.graph_order%27][num_rows$eqall]
  • Developing Human Brain Atlas ontology (as a hierarchically structured json file)
    http://api.brain-map.org/api/v2/structure_graph_download/16.json
  • Example python code to download structure information and ontology from the Allen Brain API
    http://download.alleninstitute.org/informatics-archive/allen_human_reference_atlas_3d_2020/version_1/examples/convert_to_itksnap/convert_to_itksnap.py

Transcriptional profiling: RNA-Seq Data

File Size Type Description

Readme

12 KB .txt
Read-me file with additional information about the other files in this directory.
Table of cell metadata 587 KB .csv
Metadata about cells. Each entry has an _order, _label, and _color column.
Gene expression matrix 3.4 GB .tome
Gene expression matrices provided as an HDF5 file with column-indexed sparse matrices. Exon and intron counts are stored separately. 
See “readme.txt” for data access instructions.
Taxonomy of clusters 17 KB .json
Serialized cluster hierarchy with all node information embedded.
Probability matrix of cluster membership 400KB .csv
Probability matrix that each nucleus will be in each cell type.
Taxonomy information 1 KB .txt
Metadata about the taxonomy.
Gene Expression by Cluster, trimmed means 11 MB .csv
Gene expression aggregated per cluster, calculated as trimmed means.
2D coordinates 977 KB .csv
TSNE coordinates for each cell, as shown in the Transcriptomics Explorer.