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Cell Type Annotation

Cell Type Annotation

The cell annotation model was co-developed by 10x Genomics and the Cellarium AI Lab at the Data Sciences Platform of the Broad Institute. The model is in beta. A preprint describing the method is now available on bioRxiv: Accelerating scRNA-seq Analysis: Automated cell type annotation using representation learning and vector search.
When you enable cell type annotation, your data is securely transmitted to 10x Genomics Cloud Analysis. Since your data is leaving your local environment and entering the 10x Genomics domain, it becomes subject to the terms outlined in the 10x Genomics End User License Agreement (EULA). Please review the EULA carefully to understand how your data will be handled and the associated usage terms. Additionally, please only use this feature if there are no restrictions that preclude your data being sent outside your local environment. The availability of automated cell annotation is subject to restrictions based on U.S. or local laws and regulations. See regional restrictions for the list of impacted regions.

Cell type annotation refers to the process of categorizing and assigning cell types to individual cells based on their gene expression profiles. These annotations are needed for understanding the cellular composition and diversity within a sample.

Cell Ranger v9.0 introduced support for automated cell type annotation as part of cellranger multi and cellranger count commands and as a standalone command, cellranger annotate.

To generate automated cell type annotations, ensure the following requirements are met:

  1. Your analysis includes a Gene Expression library.
  2. The total number of cells in your analysis ranges from 100 to 1.2 million.
  3. You have a 10x Genomics Cloud Analysis account.

To run automated cell type annotations with the cellranger annotate command, you will need to access the 10x Genomics Cloud CLI Access Token.

There are two ways of accessing the token:

  1. Run cellranger cloud auth setup (recommended):

Cell Ranger v9.0 introduces a new command, cellranger cloud auth setup, to simplify the process of authenticating with 10x Genomics Cloud Analysis. This command provides an interactive walkthrough that guides you step-by-step through the setup.

When you run the command:

  • You will be prompted to visit the 10x Genomics Cloud Analysis site, where you can generate an access token.
  • After copying the token, paste it back into the command prompt, allowing Cell Ranger to save the token locally.

Once saved, the token is automatically reused for future requests, making it easier to access Cloud Analysis services without needing to repeatedly enter credentials.

  1. Manually create a token file

The token is located on the security page of your Cloud Analysis account: https://cloud.10xgenomics.com/account/security.

You have the option to either generate a new token or copy an existing one.

To create a new token, click "Generate New Access Token."

Once the token is generated, use the copy button to copy the entire token and save it as a plain text file in a secure location that others cannot access. This token controls access to data stored in your 10x Cloud Account.

This token file is required as an input with a local installation (i.e., not running in 10x Cloud) to run cellranger annotate, cellranger multi, and cellranger count. When using these pipelines, you will provide a path to the token file via the --tenx-cloud-token-path argument.

The inputs for cellranger annotate are files generated by the cellranger count or cellranger multi pipelines. Therefore, before running cellranger annotate, you must first run either the cellranger count or cellranger multi pipeline.

Specifically, cellranger annotate requires the following files, located in the outs/ directory of a typical cellranger count or cellranger multi run:

  • Filtered feature-barcode matrix in H5 format
  • Loupe Browser file (.cloupe) (Optional): If you want cellranger annotate to generate an annotated .cloupe file as part of the output, you need to include this file as an input. The .cloupe file provides a visual representation of the gene expression data, which can be used in the Loupe Browser to explore the results interactively. If you do not provide a .cloupe file, cellranger annotate will still run, but it cannot produce an annotated .cloupe output.

Visit the command line arguments page for a full list of accepted arguments.

An example command looks like this:

cellranger annotate --id=sample123 \
    --matrix=filtered_feature_bc_matrix.h5 \
    --cell-annotation-model=auto \
    --tenx-cloud-token-path=/path/to/10xcloud_token.json

In this example:

  • --matrix specifies the path to the filtered feature-barcode matrix in H5 format.
  • --cell-annotation-model determines the model used for cell type annotation. When set to auto, the pipeline automatically selects the default model.
  • --tenx-cloud-token-path is the path to the 10x Genomics Cloud Access Token, which is necessary for communication with the cloud-based cell annotation model. If not supplied, will default to the location stored through cellranger cloud auth setup. If the token file does not exist, there is an error.

Cell type annotation generates the same output files, whether run as a standalone command or integrated into the count pipeline. When enabled within the multi pipeline, the annotation summary is embedded into the multi web summary HTML, with no additional web summary HTML generated. All outputs are saved in the outs/ directory.

outs/
├── cell_types
│   ├── cell_annotation_differential_expression.csv
│   ├── cell_annotation_results.json.gz
│   ├── cell_types.csv
│   └── web_summary_cell_types.html
├── web_summary_cell_types.html -> cell_types/web_summary_cell_types.html

For more details about these output files, see the Cell Type Annotation Outputs page.