Atlas: Allen Brain Cell Atlas, whole mouse brain, dataset MERFISH-C57BL6J-638850 (release 20241115), one adult male C57BL6J mouse, 59 coronal sections.
Assay: MERFISH (multiplexed error-robust fluorescence in situ hybridization) - single-molecule RNA imaging. Every cell's position is measured in tissue, not computationally placed.
Coordinate frame: Allen Mouse Common Coordinate Framework v3 (CCFv3), millimeters. Bounds here: x 0.46-10.63, y 1.39-9.27, z 0-15 mm.
Taxonomy: official WMB taxonomy and colors from the deposit - 34 classes / 338 subclasses / 1,201 supertypes / 5,320 clusters, neurotransmitter assignments per cell.
INGESTION LEDGER - EXACTLY WHAT WE PULLED
cell_metadata_with_cluster_annotation.csv - CSV, 1.02 GB, metadata/MERFISH-C57BL6J-638850/20241115/views/. All 3,938,808 cells: CCFv3 coordinates, taxonomy ids at 4 levels, neurotransmitter, official colors.
example_genes_all_cells_expression.csv - CSV, 360 MB, same folder. Log2-normalized measured expression, 8 genes (Slc17a6, Slc32a1, Tac2, Slc6a5, Slc17a7, Slc17a8, Slc6a3, Slc6a4) for every cell. Joined to the metadata on cell_label: 0 unmatched.
C57BL6J-638850-log2.h5ad - AnnData/HDF5, 7.6 GB, expression_matrices/20230830/, the 550-gene MERFISH panel x 4,334,174 profiled cells. Used for verification and additional gene columns where the panel covers them.
WHAT STREAMS TO YOUR BROWSER
manifest.json (643 KB): taxonomy names, official colors, counts, data bounds.
8 binary shards, 78.8 MB total: every cell as a 20-byte record - 16-bit CCFv3 position, taxonomy ids, neurotransmitter, and the 8 genes quantized to 256 levels. No server-side rendering; your GPU decodes and draws all 3,938,808 points.
centroids.json: the true centroid of all 338 subclasses and 5,320 clusters, computed from the cells - that is what the search box dives to.
REVIEW NOTES (FOR SCIENTISTS)
Gene-positive counts = cells with measured normalized expression > 0 for that gene. Dopamine card: Slc6a3 > 0 = 217,516 cells. The 256-level quantization preserves the positive/zero boundary exactly (verified: identical counts before and after packing).
Excite/inhibit: glutamatergic = Glut + Glut-GABA (1,393,153); GABAergic = GABA + GABA-Glyc + Glut-GABA (844,132). Co-releasing cells are counted in both groups, so the shares are of the combined 2,237,285, not of all neurons.
Non-neuronal cells (1,684,596, no assigned neurotransmitter) are included in every view and every total.
Position quantization for GPU transfer: 16-bit per axis over the data bounds, worst-case error about 0.16 microns. No downsampling: all 3,938,808 cells are rendered.
The 550-gene panel does not include Agrp, Npy, Pomc, or Gcg. Any hunger/satiety scenes on this site therefore show real taxonomy-defined populations or panel genes (e.g. Cartpt, Th, Dbh), and captions say which is which.
Reference: Yao, Z., van Velthoven, C. T. J., Kunst, M., Zhang, M., et al. (2023). A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. Nature, 624, 317–332. doi:10.1038/s41586-023-06812-z
Coordinates: Allen Mouse Common Coordinate Framework (CCFv3), mm. Colors: official WMB taxonomy colors from the deposit.
License: CC BY-NC 4.0 (Allen Institute). All counts on this page recomputed from the deposited files.
Built by Artemis BioLabs. Every dot is one measured cell — nothing generated, nothing sampled.
connecting…
Allen Brain Cell Atlas · whole-mouse-brain MERFISH Yao et al., Nature (2023) · packed binary, streamed
