Allen Brain Cell (ABC) Atlas

* The ABC Atlas empowers researchers worldwide to explore and analyze multiple whole-brain datasets simultaneously, with many millions of cells accessible at once, in a web browser.
* The ABC Atlas provides a highly intuitive and user-friendly tool for visualization of cell types and gene expression in cell-resolution spatial transcriptomics data.
* This open science resource connects to the Allen Institute’s Brain Knowledge Platform, allowing for frequent updates to include new features and data sets.

* Identify cell types located in a specific brain region and their spatial relationships
* Determine where in the brain specific cell types are located
* Refine boundaries and knowledge of brain regions defined by gene expression
* The ABC Atlas helps researchers to annotate and interpret their own data visual comparison tissue images showing specific cell populations or gene expression with presented MERFISH tissue sections

* The ABC Atlas provides helpful data for researchers designing their experiments. For example, if a researcher is interested in studying a specific population of cells in particular area of the brain, they can use the ABC Atlas to search for genes to target. Once they find potential genes, they can then look for mouse lines or antibodies to label those cells for their experiments. For example, if a researcher is interested in studying the effects of opioid signaling on sensory processing, they can use the ABC Atlas to search different genes involved in the opioid system and where they are expressed in the brain. ABC Atlas shows that Pdyn, which produces the opioid polypeptide hormone prodynorphin, is expressed in the primary somatosensory cortex. Now that they know opioid signaling occurs in the primary somatosensory cortex via prodynorphin, they can design experiments to test the function of Pdyn+ cells on somatosensory processing by using a Pdyn-Cre transgenic mouse line, stereotactic injections of Cre-dependent opsin-expressing AAVs, optogenetics, and sensory-dependent behavioral tasks.

* The ABC Atlas helps researchers further understand their own data. For example, if a researcher is creating a novel transgenic mouse line that only expresses GFP in Moxd1+ cells, they can compare their GFP expression in the novel transgenic brain with the Moxd1 expression in the ABC Atlas. Similarly, the researcher could compare the GFP fluorescence in their cells with cell type assignments for spatially localized cells in the ABC Atlas to see which cell types match the GFP fluorescence patterns. If the researchers notice a significant difference in spatial expression of Moxd1 or cell type patterning from their expectations, then they can do further experiments to determine if their GFP expression is leaky and why. The same logic could be applied to researchers who are developing novel enhancer-dependent AAVs to target specific genes or cell types of interest as well.

* The ABC Atlas helps researchers gain both a broader and deeper understanding of the brain areas and cells that they study. For example, a graduate student who does experiments on MGE-derived GABAergic cells in the primary visual cortex has likely done most of their literature review on those cells in that brain region. Instead of conducting multiple literature reviews on different brain areas to learn more about MGE-derived GABAergic cell expression across the brain, the ABC Atlas provides a “one stop shop”; any researcher can search a gene, see its expression across the whole brain, see which class/subclass/supertype/cluster of cells this gene is expressed in, see which other genes are co-expressed in these cells, and see which neurotransmitters these cells have. If this graduate student has studied MGE-derived GABAergic cells as one singular group, they can also use the ABC Atlas to gain a deeper understanding of the genetic diversity within the group by learning about the subclasses, supertypes and clusters within the MGE class.”

* Human

* Mouse

* The ABC Atlas provides a fast, web-based tool for visualization of spatial and single-cell transcriptomics data that can handle multiple data sets and millions of cells simultaneously, providing a robust platform for exploring the ever-growing whole brain data sets.
* This tool is one of the easiest online tools for exploring spatial transcriptomics data, as it does not require any knowledge of coding and can be accessed directly in a browser.

* The ABC Atlas currently explores select Allen Institute and BRAIN Initiative Cell Atlas Network (BICAN)-generated data sets ingested in the Brain Knowledge Platform, while other tools need to be used for exploring other data, including other Allen Institute or BICAN datasets and user-generated data.
* This tool is ever-growing, so please provide feedback if there are features of this tool that you’d like to see which currently aren’t implemented.

* Internet connection

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

Meng Shang, 2023, A molecularly defined and spatially resolved cell atlas of the whole mouse brain, Nature, https://www.nature.com/articles/s41586-023-06808-9

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

GitHub repository for data access, https://alleninstitute.github.io/abc_atlas_access

Allen Brain Map Community Forum, https://community.brain-map.org/c/how-to/abc-atlas/19

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, https://alleninstitute.org/events/describe_your_neurons/

Future webinar series: “Cell Type Taxonomies A-Z”” in 2024 with ABC Atlas as main topic in May 2024 and more workshops planned after May 2024 (Will be recorded for later viewing), https://alleninstitute.org/events/cell_type_az_webinars/

https://newyorkfolk.com/tech/week-in-review-most-popular-stories-on-geekwire-for-the-week-of-dec-10-2023/

Media: “BICCN: The first complete cell census and atlas of a mammalian brain” (related to two ABC Atlas data sets), https://www.nature.com/immersive/d42859-023-00069-2/index.html

Media: “Researchers map the entire mouse brain cataloging 5322 different types of cells” (related to two ABC Atlas data sets), https://www.geekwire.com/2023/entire-mouse-brain-cell-map/”