| name | iblatlas-genomics-agea |
| description | Load the Allen Gene Expression Atlas (AGEA) volumes using iblatlas. Use when the user asks to load AGEA, gene expression volumes, or the gene expression atlas. |
| allowed-tools | ["Read"] |
name: ea-load-gene-expression-volumes
Load AGEA (Allen Gene Expression Atlas)
Read sources/examples/02_download_gene_expression_atlas.py for the canonical pattern and adapt it to context.
Outputs
| Variable | Description |
|---|
df_genes | DataFrame with one row per gene; key column: gene (gene symbol string) |
expression_volumes | Array of 3-D volumetric gene expression data, indexed by row position in df_genes |
agea_atlas | AllenAtlas-like object with .bc coordinate converter and .plot_cslice / .plot_sslice methods |
Key points
label='processed' loads the denoised expression volumes; omit for raw.- Select a gene volume by index:
igene = np.where(df_genes['gene'] == 'Slc17a7')[0][0], then expression_volumes[igene].
- Coordinates via
agea_atlas.bc: .x2i(), .y2i(), .z2i() convert MNI metres → voxel indices.
- Pass a gene volume directly to
agea_atlas.plot_cslice(y, volume=expression_volumes[igene], cmap='Blues').
