MapMyCells

* With MapMyCells, neuroscientists can compare their own data to massive, high-quality, and high-resolution cell type taxonomies in mouse and human brain.
* MapMyCells will speed up the creation of brain reference atlases by facilitating the integration of community brain data with a shared reference.
* MapMyCells allows groups studying brain disease to align on common cell types to understand how these cells change in that disease.

* Assigning Allen Institute cell types to a new set of 10x data derived from mouse or human brain tissue.
* Mapping data from multiple disease studies to the same reference to determine whether changes with disease affect common types across studies.

* MapMyCells allows users to assign cells to a common set of cell types. The Allen Institute and BICAN have defined and named cell types in mouse and human brain that are currently being used by several groups in the field and that are available for viewing in the Allen Brain Cell Atlas. One challenge in the field right now is that most new papers cluster and name cell type independently, making it a challenge to compare data between studies. MapMyCells provides an easy-to-use tool for applying such “reference” cell type names to your own novel data. For example, your lab has generated a new mouse with a GFP reporter, has collected fluorescent cells from hippocampus, and has run sequencing on 10x Genomics labelled cells collected from by this genetic line. You could convert your data to h5ad format (following the online tutorial), upload your data to MapMyCells and map it against the Allen Mouse Whole Brain, and then download cell type names and confidences for every uploaded cell. This could be used both for quality control and for cross-study comparison, and could circumvent the need for clustering at all. For example, cells mapping to brain regions adjacent to hippocampus could indicate an imperfect dissection, while cells mapping with very low confidence could represent low quality cells or novel cell types, and all of these cases would warrant further analysis. Furthermore, the cells that do map to expected types could be directly compared against other papers using the same nomenclature, allowing knowledge of these types to be easily pooled between studies, and integration of novel data from your data set with what is already known about these types.
* MapMyCells can retro- or prospectively align cell type-specific changes in Alzheimer’s disease from multiple studies. Several published papers currently point to gene expression and abundance changes of specific cell types in Alzheimer’s disease (AD). In particular, there is overwhelming evidence of activated microglia and astrocytes that are quite rare in healthy brain are more common in AD. However, each of these papers uses different clustering results and nomenclature to show this, so the question remains about whether it is the same subset of glia types changing with AD in these different studies. One could use MapMyCells to map the data from all of these papers to the SEA-AD taxonomy and see (1) exactly which cells map to which SEA-AD glial types and (2) whether the cells defined as activated microglial types in other studies all align to the same cell types in the SEA-AD taxonomy. While this specific example is for AD, such an analysis could be done using any brain disease that has public data from multiple groups, or where new data is being generated.

* Human
* Mouse

* MapMyCells provides a fast, web-based tool for mapping your own data to reference taxonomies hosted by the Allen Institute for Brain Science.
* It is easy to use, as it does not require any knowledge of coding and can be accessed directly in a web browser through a straight-forward two-step user interface.
* The tool accepts up to 327 million cell-gene pairs from your own data for comparison in a single upload.
* Methods and data used in this tool are being made publicly accessible for code-based applications as well.

* MapMyCells currently includes select Allen Institute and BICAN-generated data sets ingested in the Brain Knowledge Platform, while other tools need to be used for mapping against other reference taxonomies or using different mapping algorithms that currently aren’t implemented.
* Steps before and after the mapping are not included in MapMyCells, although tutorials are provided for common applications.

* Requires an internet connection
* Data must be in anndata (h5ad file) format and include at minumum X, var_names, and obs_names parameters. Data files are capped at 500MB.
* See the help page for more details on input file requirements, limits, and creation: https://portal.brain-map.org/explore/file-requirements-and-limits.

Zizhen Yao, 2023, A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain, Nature, https://www.nature.com/articles/s41586-023-06812-z

Mariano I. Gabitto, 2023, Integrated multimodal cell atlas of Alzheimer’s disease, bioRxiv, https://doi.org/10.1101/2023.05.08.539485

https://portal.brain-map.org/atlases-and-data/bkp/mapmycells/mapmycells-use-case-single-cell-genomics-in-mouse

Input file requirements, limits, and creation, https://portal.brain-map.org/explore/file-requirements-and-limits

Available cell type references, algorithms, and output files, https://portal.brain-map.org/explore/cell-type-references-and-algorithms

Benchmarking of algorithms, http://allenbenchmark.org/

GitHub repo for the Correlation & Hierarchical Mapping algorithms, https://github.com/AllenInstitute/cell_type_mapper

Additional mapping algorithms (R package), https://github.com/AllenInstitute/scrattch.mapping/

Additional published Allen Institute taxonomies and associated taxonomy format, https://github.com/AllenInstitute/scrattch.taxonomy/

Allen Brain Map Community Forum, https://community.brain-map.org/c/how-to/mapmycells/20

Past workshop: “Navigation and applying cell type taxonomies and tools from the Allen Institute for Brain Science” at IBRO 2023, https://alleninstitute.org/events/ibro2023/

Past workshop: “Satellite Event: Open resources for cell types and taxonomies with the Allen Brain Map” at SfN 2023, https://alleninstitute.org/events/sfn2023/

Future workshop: “Describe Your Neurons Like the Allen Institute” at the Allen Institute April 2024 (Will be recorded for later viewing), https://alleninstitute.org/events/describe_your_neurons/

Future webinar series: “Cell Type Taxonomies A-Z”” in 2024 with MapMyCell as the main topic in April 2024, https://alleninstitute.org/events/cell_type_az_webinars/