ibl-anatomy

name	ibl-anatomy
description	Use this skill to navigate the IBL anatomical atlas — region lookup by name/id/coordinate, hierarchy traversal, mapping between Allen/Beryl/Cosmos/Swanson, and brain-map visualisation.

IBL Anatomy

Use this skill when

• Converting between region acronyms, IDs, and atlas mappings.
• Looking up which region contains a CCF coordinate.
• Traversing the region hierarchy (ancestors, descendants, leaves).
• Visualising per-region scalars or point clouds on slices, flatmaps, or Swanson projections.

Do not use this skill when

• The task is spike-sorting QC or cluster-to-region assignment — use ibl-load/references/brain_regions_qc.md.
• The task is raw Neuropixels preprocessing — use ibl-neuropixel.

References

• references/atlas_navigation.md: verified API patterns for BrainRegions, AllenAtlas, and iblatlas.plots.

Workflow

1. Use BrainRegions alone when no coordinate lookup is needed — no file I/O.
2. Instantiate AllenAtlas(res_um=25) only when CCF volume, slicing, or get_labels is required.
3. Declare one mapping per metric before any groupby: Allen, Beryl, Cosmos, or Swanson (+ -lr variants for hemisphere-sensitive analyses).
4. For hemisphere-aware plots, use prepare_lr_data and a -lr mapping; note that -lr encodes left as negative ID.
5. Use iblatlas.plots helpers before writing custom matplotlib; prefer plot_points_on_slice for coordinate clouds and plot_swanson_vector for Swanson projections.

Quality gates

• Never mix IDs or acronyms from different mappings in one aggregation.
• State the mapping used in every region-level output and figure caption.
• All coordinates passed to iblatlas must be in metres, bregma-relative, axis order (ML, AP, DV).