DigitalBrain Data Explorer

Single-Cell Brain Dataset Explorer

Donor-normalized cohort views for harmonized single-cell brain data across collections, datasets, and disease conditions.

Gene expression is a cross-study merge with the dataset axis collapsed, so it is always shown at global scope. Collection, dataset and donor filters do not apply to this layer.

Current Scope

All Collections

Use the filters above to move from collection-level summaries down to donor-specific views.

The 3D atlas is shown first. Switch to Overview here for cell-type and brain-region charts.

Datasets 0
Donors 0
Cells 0

Collection Overview

Datasets 0
Donors 0
Total Cells 0
Brain Regions Brodmann 0 Gyral 0
Cell Types 0

Dataset Overview

Donors 0
Total Cells 0
Brain Regions Brodmann 0 Gyral 0
Cell Types 0

Donor Details

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Age: - Gender: -
0 cells

Cell Type Distribution

Composition, diversity, and comparison views for the current scope.

Brain Region Distribution

Composition, coverage, and comparison views for regional annotations.

Please select a collection to view data
Interactive 3D Atlas
Whole-brain cells + Allen 3D anatomy 105 profiles placed
105 31 cell types

Cell type
Cell type

Tick any number of classes: the atlas is recoloured from those alone, not just the detail panel. “only” isolates one class.

0%
0%100%
96%
0%100%

55 regions shared by the FC and SC matrices

Label DMN nodesCore and associated nodes in this atlas vocabulary
3D anatomyOfficial Allen voxel geometry
Region envelopesFilled parcel boundary overlays
Auto-rotatePause automatically on selection
i

Anatomy is derived from the Allen Human Reference Atlas – 3D, 2020. When linked to a selection, only sampled regions are shown (sized by cell count); composition is scope-level (marginal), not region-resolved.

Functional focusMemory—
No regions match the current filters.
SA
Excitatory neuron12–52%
LowerRelative abundanceHigher
All cell typesWithin-region composition
Gene expressionMean expression
SparserLit point densityDenser
Functional connectivityTop 4%
P96Within-matrix percentileP100
≥ 0.3893.800
— links
DMN nodeFunction-focused link
Anatomy parcelParcel boundaryCell profile
Exact anatomyCoarse ontology proxyCurated gyral proxy
Drag to rotate anatomy · Scroll to zoom · Click a cell-profile marker

Select a region

Select a mapped parcel to inspect its anatomical support and cell-class profile.

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Excitatory neuron—
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Region role and functions

Curated context

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Selected genes here

Mean expression

Cell-class composition

Relative proportion

Member regions

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Strongest connections

Weight

Selected connection

FC
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fMRI FC weight
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Matrix percentile
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Descriptive association only; no direction or causality is implied.

Atlas context

Region universe
Table 2 hierarchy
Spatial layout
Allen 3D mapping
Mapping basis
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Data status
Illustrative

Across brain regions

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Housekeeping genes are drawn as reference bars, never as part of the selection. Classic controls (ACTB, GAPDH) are the familiar ones but vary 2.5-2.8x between brain cell types; the stable set varies 1.4-1.7x and is the one to trust when the levels matter. In the type panel each control is read in that type, so it shows how low the baseline sits there before any gene is compared against it.

Within cell types

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Data and interpretation

A scientifically cautious prototype

Region identities come from the 106-region DigitalBrain hierarchy. When linked to a Data Explorer selection, sampled regions are matched on the Brodmann axis and sized by real per-region cell counts.

Cell-type composition uses the Data Explorer's original taxonomy. Because the source data stores only marginal distributions (region totals and cell-type totals, not a joint region × cell-type matrix), the per-region composition shown is scope-level, not region-resolved.

Functional and structural connectivity are read from the project's 55-region FC and SC matrices; links are undirected and descriptively thresholded by matrix percentile.