View brains and atlas data
Open a brain from the catalogue, or select an atlas release and variant. BrainMaps uses Neuroglancer to stream supported volumes, segmentations and meshes without downloading the whole dataset first.
Anatomy, channels and overlays
- Anatomy focuses on 3D anatomy. Where region meshes and label metadata exist, regions use their supplied colours and names.
- Channels displays image channels and their controls.
- Overlay combines available image and anatomical layers.
Multichannel volumes default to a 3D view when no explicit saved layout takes precedence. The Channels and Overlay presets currently select Slices; select 3D afterwards to use their layers in the 3D panel. A saved viewer state can restore its own layout and layer settings.
Channel controls and voxel values
Image channels can be shown or hidden independently and assigned display colours. Intensity-range, contrast, brightness and opacity controls change their appearance; volume-rendering controls tune the 3D view. These display settings do not rewrite the source voxels.
Use a slice view to inspect a voxel value. The readout comes from the currently loaded resolution level. At coarse zoom it can be a downsampled value; zoom in to the finest level before comparing it with a full-resolution measurement.
A 3D projection combines samples along a viewing ray and does not identify a unique source voxel at each screen pixel. Use slices for an unambiguous location/value check.
Automatic resolution selection
Neuroglancer automatically chooses among pyramid resolutions advertised by the dataset’s multiscale metadata. It requests coarser data when zoomed out and finer data as you zoom in. Rendering detail settings can also affect the selected level.
The viewer does not generate missing pyramid levels. A single-resolution dataset remains single-resolution; missing or incorrect multiscale metadata can prevent automatic selection. Preserve valid OME-Zarr multiscales or build a precomputed pyramid during conversion.
Meshes, segmentation and image volumes
| Data available | What you can do |
|---|---|
| Region meshes and label table | Explore coloured 3D structures and names |
| Voxel segmentation | Overlay region IDs on slices and link voxels to labels |
| Image volume and channel metadata | Inspect intensities and render channels in slices or 3D |
| Image pyramid | Stream different levels of detail as you zoom |
| Registered layers and transforms | Compare data in a shared reference coordinate space |
Some imported atlas variants currently contain meshes only. They do not thereby include a reference-intensity volume, voxel segmentation or a registration target. Choose the correct variant and inspect its available assets.
Coordinates and registration
Use Native coordinates for the original specimen and the relevant registered reference space when a registration result exists. Two layers can be visible together while still being misaligned. Matching physical units, orientation, origin and a valid transform are required for meaningful overlays. See registration.
Transcriptomics
Fluorescence channels such as antibody markers are image intensities, not a gene-expression matrix. A layer marked transcriptomic can display prepared spatial labels, but the current viewer has no general expression-matrix import or gene-query interface.
To add spatial transcriptomics meaningfully, the data need cell/spot identifiers, gene-expression values, spatial coordinates with units, and a transform into the specimen or atlas coordinate space. Those data and the corresponding ingestion/query UI are required before the platform can offer a complete gene-expression explorer.
If data do not appear
Sign in first for protected datasets. Check that the selected variant actually includes the desired layer, that its source URL is reachable with suitable CORS, and that its coordinate scale matches the other layers. Missing source data cannot be recovered by changing viewer controls.