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. |