MapMyCells

MapMyCells transforms cell types from a concept in publications to a tool for public research. Scientists worldwide can discover what cell types their transcriptomics and spatial data corresponds with by comparing their data to massive, high-quality reference datasets, including the Allen Institute’s whole mouse brain multi-omics atlas, which was developed as part of the NIH’s Brain Initiative Cell Census Network and an atlas of cell types in the cortex of aged humans, which was developed as part of the Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) consortium. Both datasets are also available Allen Brain Cell Atlas.

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What is MapMyCells?

MapMyCells allows users to assign cell type names from Allen Institute-hosted taxonomies to their own single cell and spatial transcriptomics data. Such data integration allows users to leverage additional community knowledge and data visualizations in their own research. Read more about MapMyCells and related resources here.

Learn more Available taxonomies Available algorithms Cite this tool

Using MapMyCells

MapMyCells includes a drag-and-drop interface for users to assign cell type names from the above taxonomies to their own data. Files up to 2GB or about 150,000 cells can be processed through the browser. There is also a more flexible code-based implementation. We recommend first time users start with the step-by-step guide, which describes file formats, use cases, and additional options.

A step-by-step guide to using MapMyCells

Go directly to the MapMyCells UI Run the code on your own

How to get help

Learn how to use MapMyCells from existing videos, review frequently asked questions in the step-by-step guide above, or reach out to the scientists and MapMyCells team directly on the Community Forum.

MapMyCells webinar (47 min) Video tutorial (24 min) Community Forum