ABC Atlas Update Notes - May 14, 2024

The Allen Brain Cell Atlas (ABC Atlas) has been updated with new features and improvements!

Anatomical Annotations

With this release we introduce the ability to view spatial data with anatomical annotations.

The first data set to support these annotations is the MERFISH Spatial Transcriptomics Dataset of a Single Adult Mouse Brain registered to the Allen Mouse Brain Common Coordinate Framework (CCFv3).

The CCF is an annotated 3D reference space with 10µm voxel resolution. An average template brain was created from images of 1,675 young adult C57BL/6J mouse brains acquired using serial two-photon tomography.

Using multimodal reference data (e.g., histological stains, immunohistochemistry, transgene expression, connectivity patterns, endogenous gene expression) we parcellated the entire brain directly in 3D, labeling every voxel with a brain structure spanning 43 isocortical areas and their layers, 329 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures.

Registration to the whole mouse brain was applied at a coarse level to account for brain size, sectioning angle and location of major anatomical division. Cell types based anatomical landmarks were used to further refine registration in the isocortex and thalamus. Regions around tissue artifacts may result in alignment anomalies.

Selecting the data set
To view the CCF annotations, select the MERFISH-C57BL6J-638850 Reconstructed Coordinates dataset from Manage Layout Add Visualization menu.

Annotation tool tips
When hovering over a cell, the anatomical annotation for that region will also be displayed.

Annotation controls
For datasets that support anatomical annotations, a new pen icon will be available in the top left of the view. Click this icon to manage annotation settings

  • Change the granularity level of the regions using the drop down menu.
  • Select whether the annotations appear as an overlay (in front) or and underlay (behind) the cell dots.
  • There are two display options for annotations which can be used separately or together.
    • Stroke will display outlines of the anatomical regions
    • Fill will show a solid color in each region.
  • The transparency of both the outlines and the fill can also be changed by specifying an opacity percentage next to the droplet.
  • The (i) icon shows additional information about the annotation data (e.g. version numbers), if available.
    Undo and Redo
    Actions taken to change views can now be reversed. Actions include applying filters, adding or removing views, changing pan and zoom camera positioning, and more. To undo previous actions, click the back arrow in the bottom of the left-most navigation panel. Once an action has been undone, it can be redone by clicking the forward arrow.


As always, thank you for being part of the AIBS community. Please let us know how we can improve the ABC Atlas to better serve your needs.

For complete user guide documentation see the ABC Atlas User Guide.