int-brain-lab/iblatlas/iblatlas-genomics-agea

Claude Code and agent skill by int-brain-lab/iblatlas

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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.

Install

npx vskill@latest install int-brain-lab/iblatlas/iblatlas-genomics-agea

SKILL.md

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

VariableDescription
df_genesDataFrame with one row per gene; key column: gene (gene symbol string)
expression_volumesArray of 3-D volumetric gene expression data, indexed by row position in df_genes
agea_atlasAllenAtlas-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').

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