HMBA Basal Ganglia: Neuroglancer Views

Quick Guide

Click a section title to expand/collapse.

1. Filter annotations by cell types

1. From the right pane, pick taxonomic cell types to show or hide (yellow box).
2. To filter cell types by taxonomic level, click the + or − buttons next the taxonomic level (red box).
3. If right panel is not visible, right-click the cell_types tab on the top left.
4. In that panel, select the seg tab.

2. Color annotations by taxonomic level; set annotation size & opacity

1. Select the cells tab from the top left, then choose the rendering tab in the right pane.
2. Choose a taxonomic level for coloring with the level_color_selector:
   • 1: Neighborhood
   • 2: Class
   • 3: Subclass
   • 4: Group (default)

   

3. Adjust annotation size and opacity.

3. View annotation metadata

To see metadata for an annotation:

1. Click the hamburger icon (third icon) from the top right to toggle Selection Details Panel.

2. Mouse over an annotation to view its metadata from the right panel.

4. Align view with cell sections by tilting cross-section plane

Tilting the cross-section plane helps match views to cell section planes.

1. Click inside a view (coronal, transverse, sagittal) to focus it.
2. Rotate with keys: e (left) and r (right).
3. Alternatively, hold Shift and drag with the mouse to tilt across all axes.

Before tilting

After tilting

5. Increase annotation view depth

If only a partial coronal cell-section plane is visible, increase the annotation view depth.

Shortcut: Hold Alt and use the mouse wheel.

Neuroglancer views - coordinate spaces

Click thumbnails to launch Neuroglancer for each coordinate space

The cell coordinates are registered to four different reference spaces, each serving a distinct purpose.

Slab

The coordinate system of the slab face images that each spatial transcriptomics plane belongs to.
This view shows cells in the context of the imaging assets used for mosaicking (e.g., block-face and slab-face images).

Donor

The native MRI space corresponding to the individual donor from whom the spatial transcriptomics sections were sampled.
This view preserves subject-specific anatomy before normalization to any common template.

CCF (Common Coordinate Framework)

The standardized reference space for the donor’s species, enabling cross-donor and cross-dataset comparisons.
See this link for more details.

HiP-CT (Cellular-Resolution Volumetric Scan)

A cellular-resolution (25 µm) volumetric scan of the human brain.
Details about the HiP-CT dataset and donor.
Note: The spatial transcriptomics data were not sampled from the same donor; alignment is used only for anatomical correspondence.

Species	Donor	Slab	Donor	CCF	HiP-CT
Human	H22.30.001		—
Macaque	QM23.50.001 (Red)		ETA 2026	ETA 2026	TBD
Marmoset	CJ23.56.004 (Tank)		ETA 2026	ETA 2026	TBD