Human-Mammalian Brain - Basal Ganglia: spatial transcriptomics cells for each species#

Data and metadata for the spatial component of the Human and Mammalian Brain Atlas - Basal Ganglia (HMBA-BG) dataset.

The basal ganglia are a set of subcortical structures critical for motor control, particularly in the context of action selection, motor learning and emotional state, whose coarse functional organization is well-described in the literature. Although single-cell RNA-Seq studies have greatly enhanced our understanding of cellular diversity in the brain, the exact spatial distribution of cell types within the brain has been difficult to determine. Using spatial transcriptomics platforms such as MERSCOPE or Xenium enabling spatial profiling of hundreds of genes for each cell, and the mapping the cells to the consensus basal ganglia cell type taxonomy.

These data form the basis of the cross species Basal Ganglia (BG) taxonomy.

For more information on the taxonomy, please refer to the following webpage: Mammalian Basal Ganglia Consensus Cell Type Atlas. Additionally, you can see the associated notebooks linked at the end of this page.

The expression matrices and associated metadata are hosted on AWS S3 bucket as a AWS Public Dataset. We’ll describe each component below.

The three species are broken up by their donor ID. These are:

  • Human: H22.30.001

  • Macaque: QM23.50.001

  • Marmoset: CJ23.56.004

Each release directory also includes the name of the platform used, either MERSCOPE (Human and Macaque) or Xenium (Marmoset).

Below are links to the directories containing h5ad files of the expression matrixes for each species both the raw counts and the log2 of the counts per million for each cell.

Component

Current Version

Size

Human: Expression Matrices

s3://allen-brain-cell-atlas/expression_matrices/HMBA-MERSCOPE-H22.30.001-BG/20250930/

1.34 GB

Macaque: Expression Matrices

s3://allen-brain-cell-atlas/expression_matrices/HMBA-MERSCOPE-QM23.50.001-BG/20250630/

1.52 GB

Marmoset: Expression Matrices

s3://allen-brain-cell-atlas/expression_matrices/HMBA-Xenium-CJ23.56.004-BG/20250630/

0.61 GB

The following links contain metadata tables summarizing the cells, specimens the cells originate from, donors, and coordinates. For more information on how the metadata is laid out and examples on using and joining the different tables, see the the spatial notebooks linked below. For the metadata, a supplementary table of quality control and other metrics is available. You can find descriptions of the columns on the Resources page under Supplemental Metadata Descriptions.

Component

Current Version

Size

Human: Cell and gene metadata

s3://allen-brain-cell-atlas/metadata/HMBA-MERSCOPE-H22.30.001-BG/20250930/

2.4 GB

Macaque: Cell and gene metadata

s3://allen-brain-cell-atlas/metadata/HMBA-MERSCOPE-QM23.50.001-BG/20250630

1.4 GB

Marmoset: Cell and gene metadata

s3://allen-brain-cell-atlas/metadata/HMBA-Xenium-CJ23.56.004-BG/20250630/

762.8 MB

The links below contain geojson files that define the manually drawn polygons that represent anatomical annotation of select basal ganglia regions. These are used and tutorialized in the spatial notebooks linked at the bottom of this page. Please note that these polygons are not derived from registration to the Harmonized Ontology of Mammalian Brain Anatomy (HOMBA). They should instead be used as cellular groupings to orient the user in the anatomical context of the spatial transcriptomics data.”

Component

Current Version

Size

Human: Image volumes and polygons

s3://allen-brain-cell-atlas/image_volumes/HMBA-MERSCOPE-H22.30.001-BG/20250630/

86.6 KB

Macaque: Image volumes and polygons

s3://allen-brain-cell-atlas/image_volumes/HMBA-MERSCOPE-QM23.50.001-BG/20250630/

114.6 KB

Marmoset: Image volumes and polygons

s3://allen-brain-cell-atlas/image_volumes/HMBA-Xenium-CJ23.56.004-BG/20250630/

422.5 KB

Data is being shared under the CC BY NC 4.0 license.

Related resources:

Associated notebooks: