> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/icm/studies/view-studies/sample-metadata/cell-metadata.md). # Cell metadata ### [Publish Cell attributes to a project](/icm/analyses/analysis-functionality/task-menu/annotation-metadata/publish-cell-attributes-to-project.md) Cell level attributes can be used for filtering, cell selection, classification and differential analysis using the [Publish Cell attributes to project task](/icm/analyses/analysis-functionality/task-menu/annotation-metadata/publish-cell-attributes-to-project.md). Data nodes in the Analyses pipeline that contain this cell level information (e.g. Graph-based clusters data node) can be published to the project and will then be available in **Study > Analysis > Metadata > Manage** under Cell attributes where they can be modified and reordered. ### [Annotate cells](/icm/analyses/analysis-functionality/task-menu/annotation-metadata/annotate-cells.md) If you have attribute information about your cells, you can use the [Annotate cells task](/icm/analyses/analysis-functionality/task-menu/annotation-metadata/annotate-cells.md) in Connected Multiomics to apply this information to the data. Once applied, these can be used like any other attributes, and thus can be used for cell selection, classification and differential analysis. To run Annotate cells: * Click a Single cell counts data node * Click the **Annotation/Metadata** section in the toolbox * Click **Annotate cells** You will be prompted to specify annotation input options: * Single file (all samples): requires one .txt file for all cells in all samples. Each row in the file represents a barcode and at least one barcode column which will match the barcodes in your data. It also requires a column containing Sample ID which must match the Sample name in the Metadata tab of your project. * File per sample: requires the format of all of the annotation files to be the same. Each file has barcodes on rows, it requires one barcode column that will match the barcodes in your data in that sample. All files should have the same set of columns, column headers are case sensitive. --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation by asking a question. Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters: ``` GET https://help.bioinsight.illumina.com/icm/studies/view-studies/sample-metadata/cell-metadata.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.