MapMyCells has been updated with new data, algorithms, and features!

New Data

This is the first human reference dataset available in MapMyCells:

Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) MTG - 10x single nucleus RNAseq

This is a high-resolution transcriptomic cell type atlas from middle temporal gyrus (MTG) from the SEA-AD aged human cohort that spans the spectrum of Alzheimer’s disease. The atlas was created from a single nucleus RNA-sequencing (snRNAseq) dataset of ~2.0 million cells profiled (~1.4 million cells after QC). The atlas is hierarchically organized into nested levels of classification: 3 classes, 24 subclasses, and 139 Supertypes.

New Algorithms

Deep Generative Mapping

Deep Generative Mapping is a deep generative model algorithm for mapping snRNA-seq data sets and assigning cell type identity, based on Allen Institute-hosted reference taxonomies. Cells mapped with this method are not only assigned an associated cell type, but also associated confidence on mapping, and additional information for visualizing and quantifying the level of agreement.

Learn more about this algorithm in: Gabitto MI, Travaglini KJ, et al. Integrated multimodal cell atlas of Alzheimer’s disease. Res Sq [Preprint]. 2023 May doi: 10.21203/ PMID: 37292694; PMCID: PMC10246227

SEA-AD Correlation & Hierarchical Mapping

The Correlation & Hierarchical Mapping algorithms from the first MapMyCells release have been re-trained to now also process human data.

Learn more about these algorithms here: Cell Type References and Algorithms -

New Features

Cite this tool button.

Researchers can now easily cite MapMyCells by using the new “CITE THIS TOOL” button. It can be found at the bottom of the Step 1 section in the user interface and links to MapMyCells’ RRID entry.


Mapping outputs now in .zip file.

The mapping results package now comes in an easier to use .zip file instead of the prior .tar tarball. This also resolves a set of issues that could results from long file names.

Counts of mapping cells & genes in results table (signed-in experience)

We added a new column to the “Map Results” table that features the counts of mapped cells & genes for each run. These are intended as summary statistics and allows researchers to assess the coverage of the mapping before downloading the results for a deeper analysis.

General UI and dialog polish

We also included several smaller quality-of-life improvements:

  • Changed link styling to better highlight documentation links in light-mode color scheme.
  • New confirmation dialog prevents accidental cancellation of an in-progress mapping.
  • Consistent loading bar fixed to top of page, e.g when deleting a mapping result.
  • Reduced white space in “Map Results” table (signed-in experience).
  • Improved text wrapping in “Map Results” table (signed-in experience).

For a complete user guide documentation see the MapMyCells User Guide.

As always, thank you for being part of the AIBS community. Please let us know how we can improve MapMyCells to better serve your needs.

I am enthusiastic about utilizing MapmyCell for exploring the cell types within my research dataset. However, I would appreciate more information about the security measures of uploading my research data to mapp my cells.

Hi @KatherineMO,
Thank you for your interest in MapMyCells.

Please see the response from Elysha Fiabane in this thread:

If you have further questions, please elaborate on what security aspects you have further questions about and tag @Elysha-AIBS .