HMBA Basal Ganglia: Neuroglancer Views

Neuroglancer Views – Coordinate Spaces

Click thumbnails to launch Neuroglancer for each coordinate space.

Table 1 Neuroglancer links

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

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.

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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 by taxonomic level, click the + or − buttons next to each taxonomic level (red box).

3. If the 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. Or 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.

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