Introducing MapMyCells!

The Allen Institute for Brain Science has just released the first dataset unifying cell types and anatomy across the whole mouse brain. Now we’re releasing an additional product - MapMyCells - to automatically assign cell types to your cell data using the whole-brain taxonomy.

MapMyCells transforms cell types from a concept in publications to a tool for public research. Scientists worldwide can now 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 is available in Allen Brain Cell Atlas.

One key advantage to MapMyCells is scale: using our cloud-based Brain Knowledge Platform and reference datasets with millions of cells, researchers can provide up to 327 million cell-gene pairs from their own data, which is a huge leap forward for working with whole-brain datasets.

MapMyCells is the latest addition to a growing Brain Knowledge Platform and opens up endless possibilities for groundbreaking discoveries and breakthroughs in neuroscience. With MapMyCells, researchers everywhere can better understand their data and further advance discovery into the brain’s complex workings, growing our understanding of this amazing organ in ways we never thought possible.

We’re planning to release updated versions of reference taxonomies and algorithms as well as make additional ones available in regular intervals. We value your feedback. Please let us know what you think and what you’d like to see in future updates!

User Interface

MapMyCells offers researchers a simple two-step process to map their gene expression data against our reference taxonomies via mapping algorithms from the Allen Institute.

1.) Upload your gene expression data.

2.) Run the mapping and download your results.

Try MapMyCells now.

Learn more about the file requirements, limits, and creation as well as available cell type references, algorithms, and output files on our help pages.