Maps / H01

H01: one cubic millimetre of human cortex, mapped cell by cell

H01 is a piece of human temporal cortex, about one cubic millimetre, imaged with an electron microscope at nanometre resolution and reconstructed in 3D by Google Research and the Lichtman lab at Harvard (Shapson-Coe et al. 2024, Science). The tissue was removed during surgery for epilepsy, so it comes from a living adult human brain, and it is released openly under CC BY 4.0.

What is in it

Volumea slab about 3 × 2 mm wide and 0.17 mm thick ("just over one cubic millimetre")
Images5,019 sections, ~34 nm thick, 4 nm pixels — about 1.4 petabytes
Cells57,216 in total: 16,087 neurons, 32,315 glia, ~8,100 blood-vessel cells (paper, Table S5)
Synapses~150 million detected automatically
Layersall six cortical layers plus some white matter

How to look at it yourself

  • Neuroglancer (in the browser): the H01 team's gallery opens ready-made views — whorled axons, a dendrite through a cell body, glia glued to neurons, every blood vessel. Start at the H01 gallery.
  • Raw data: gs://h01-release/data/20210601/ (images, segmentation c3, synapses, cell bodies).
  • Two synapse releases. Only one (20210729) matches the paper's per-cell tables. We used the wrong one at first — here is how to tell them apart.

Things to keep in mind

  • One sample, one person. The tissue comes from epilepsy surgery; whether it is typical of healthy cortex is an open question the authors raise themselves.
  • Automated reconstruction. Cells can be split or merged by mistake; the "strange" structures in the gallery could be biology or glitches.
  • Edges. Cells are cut off at the sample boundary, so counts per cell are lower bounds.

Numbers we measured from H01

37%of the cells in layer 1 are astrocytes — the most common cell in the cortex's top layer
How: Cells by the dataset's layer labels (somas.csv): layer 1 — 1,688 astrocytes of 4,595 cells; 1,688 of the sample's 5,474 astrocytes (30.8%) sit in layer 1. Consistent with the paper's Table S4 (astrocyte volume fraction 21.6% in layer 1 vs 14–15% in layers 2–6).
Caveat: One sample; layer labels are the dataset's own. The map does not tell astrocyte subtypes apart (e.g. primate-specific interlaminar astrocytes, Oberheim et al. 2009).
18% vs 70%of the cells are neurons in layer 1, the cortex's top layer, versus layer 2 just below
How: Cells by the dataset's layer labels (somas.csv): layer 1 — 827 neurons of 4,595 cells (586 interneurons, 72 pyramidal); layer 2 — 4,656 of 6,651.
Caveat: Layer labels are the dataset's own; one sample. Layer 1 is mostly wiring: pyramidal-cell branch tips meeting long-range inputs (Schuman et al. 2021).
20,139 vs 16,087oligodendrocytes outnumber neurons in this human cortex sample
How: Cell types in H01 somas.csv; matches the paper's Table S5 exactly.
Caveat: Driven by the white matter in the sample: in the grey-matter layers alone neurons outnumber oligodendrocytes (15,005 vs 9,350).
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77%of the cells in the sample's white matter are oligodendrocytes
How: 10,110 of 13,063 white-matter cells in somas.csv (half of all oligodendrocytes in the sample sit there).
Caveat: Layer labels are the dataset's own.
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98%of neurons sit within 50 µm of a blood vessel
How: 10,441 neuron cell-body centres (somas.csv, away from the sample edges) to the nearest vertex of the finest blood-vessel meshes (1,477 segments). Median 22.9 µm; max 141 µm.
Caveat: Distance to mesh vertices (spacing ~1.6 µm); the vessel segmentation may miss some capillaries, so true distances may be shorter. One ~1 mm³ sample of human temporal cortex.
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245 µm²of a glial cell's surface pressed against a neuron's cell body
How: Finest meshes of the gallery's 'parasitic_glial' cells: glial surface within 0.25 µm of the neuron (8% of the glial surface; ~5% of the neuron's cell-body surface).
Caveat: One pair of cells; the glial cell is labelled microglia/OPC.
≈7 µmacross: a flat, whorled axon coiled on a neuron's cell body
How: Finest public meshes of the gallery's 'axon_whorl' (97 segments); disc ≈6 × 7 µm, ~1.6 µm thick; checked against the raw electron-microscopy images.
Caveat: Automated segmentation; which pieces form the axon was chosen by the H01 team's gallery.
almost allinputs within 20 µm of one pyramidal neuron's cell body are inhibitory
How: All input synapses of cell 6644185383 in both public synapse releases; within 20 µm of the soma centre: 97.7% (20210601) and 96.5% (20210729, the release that matches the paper).
Caveat: One cell. Labels partly depend on whether a synapse sits on a spine.
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~150 millionsynapses in just over one cubic millimetre of human cortex
How: Paper's automated count: 149,871,669 synapses in the volume.
Caveat: Automated detection; the paper reports missed and false detections.
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