Study
Opening the study…
Study
Opening the study…
What the work was done with, as its author lists it, so someone else can get the same things and do it again.
Other
Allen MERFISH whole mouse brain C57BL6J-638850 (Yao et al. 2023)
https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/metadata/MERFISH-C57BL6J-638850-CCF/20231215/views/cell_metadata_with_parcellation_annotation.csv
CC BY-NC 4.0. Converted by code/prep.py into data/cells_allen.npz; source sha256 in data/SOURCES.json.
Other
Zhuang lab MERFISH whole mouse brains Zhuang-ABCA-1..4 (Zhang et al. 2023)
https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/metadata/Zhuang-ABCA-1/20241115/ (and -2,-3,-4; CCF coordinates; raw h5ad for per-cell transcript counts)
CC BY 4.0. Converted into data/cells_zhuang{1..4}.npz; sha256 in data/SOURCES.json.
Other
Whole mouse brain 10x taxonomy cluster means (WMB-10X precomputed stats) and gene/cluster tables
https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/mapmycells/WMB-10X/20240831/precomputed_stats_ABC_revision_230821.h5
Subclass mean expression of energy genes in data/subclass_expression.csv.
Other
KEGG pathway mmu00190 Oxidative phosphorylation
https://rest.kegg.jp/get/mmu00190
Used only to define the gene list in data/energy_genes.csv (fetched 2026-10-09 01:12 UTC; file sha256 d5e9133f...); KEGG file not redistributed.
Software
Python scientific stack
numpy scipy pandas pinned in env/requirements.txt on public.ecr.aws/docker/library/python:3.12-slim