iblatlas-genomics-merfish

name	iblatlas-genomics-merfish
description	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.
allowed-tools	["Read"]

name: ea-load-merfish-dataframes

Load MERFISH single-cell atlas

Read sources/examples/05_load_merfish.py for the canonical pattern and adapt it to context.

Outputs

Variable	Description
df_cells	One row per cell; columns x, y, z (MNI metres), class, subclass, supertype, cluster (integer keys)
df_classes	Cell-class metadata; key column: class_rgba (packed int, convert with merfish.int2rgb())
df_subclasses	Subclass metadata
df_supertypes	Supertype metadata
df_clusters	Cluster metadata
df_neurotransmitters	Neurotransmitter metadata

Key points

• Cell coordinates are in metres (MNI space); multiply by 1e6 for µm when plotting.
• Get RGB colours for scatter plots: rgb = merfish.int2rgb(df_classes.loc[df_cells['class'], 'class_rgba']).
• Filter a coronal slice: mask = np.abs(df_cells['y'] - yslice) < (30 / 1e6).
• Use df_cells['class'] as an index into df_classes (and similarly for other taxonomy levels).

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Load MERFISH cell-type density volumes

from iblatlas.genomics import merfish
volume, labels, agea_atlas = merfish.load_volume(level='class')  # denoised by default; label='' for raw

Variable	Shape	Description
volume	(n_types, dim0, dim1, dim2)	Per-voxel cell-type density
labels	(n_types,)	Type index per channel — same key space as df_classes.index above
agea_atlas	—	Atlas matching the volume grid

level is one of 'class', 'subclass', 'supertype', 'cluster'. The grid is the AGEA 200 µm grid, not the default 25 µm AllenAtlas() — index it via agea_atlas.bc. See the merfish.load_volume / merfish.denoise_volume docstrings for the label argument and denoising details, and sources/examples/08_load_merfish_volumes.py for a worked loading + plotting example.