int-brain-lab

Use this skill for quantitative scientific analysis of IBL data after the always-on scientific workflow in `AGENTS.md` is active.

Use this skill when loading IBL data, preferring the smallest sufficient local or aggregate surface before session-level loaders.

describes how to write code to be read and validated by human scientists.

Use this skill for raw Neuropixels binary access, destriping, compression, waveform extraction, and probe-level preprocessing based on the `int-brain-lab/ibl-neuropixel` repository.

Use this skill to analyze scientific data: refine, formalize and test hypotheses.

Use this skill if the required tools are not yet installed.

Use this skill when a task needs IBL data access setup, ONE/Alyx authentication, or selecting between public and private data modes.

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.

Load the Allen/Knox regularized-regression mesoscale mouse connectivity matrix and the Harris et al. cortico-thalamic hierarchy scores using iblatlas. Use when the user asks to load mesoscale connectivity, the mouse connectome, connection strength/density, or cortical/thalamic hierarchy scores.

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.

Load the MERFISH single-cell atlas (parquet dataframes) and the MERFISH cell-type density volumes using iblatlas, including how to denoise the volumes. Use when the user asks to load MERFISH, single-cell atlas data, cell-type data, MERFISH volumes, or how to denoise/preprocess them.