Resources
Authors & Affiliations
Rachel Hostetler, Lauren Alfiler, Elysha Fiabane, Julie Nyhus, Shoaib Mufti, Michael Hawrylycz, Kaitlyn Casimo, Jeremy Miller
Abstract
The Allen Institute for Brain Science uses a collaborative, big science approach to tackle complex bioscience questions. One of these questions is: “How many cell types are in the mammalian brain?” To answer this, multiple large-scale studies using single cell/nucleus RNA-seq and other data modalities have been conducted to generate cell type taxonomies. To make these datasets more accessible to the scientific community and general public, we have created open, browser-based tools for anyone to interact with the data; they are available on brain-map.org. Three of these tools are: Cell Type Knowledge Explorer (CTKE), Allen Brain Cell Atlas (ABC Atlas), and MapMyCells. The CTKE provides multimodal data on cell types in motor cortex, ABC Atlas visualizes gene expression and spatial context of cell types across the brain, and MapMyCells allows users to map Allen Institute cell type names to their own data. To increase awareness, accessibility, and usage of these tools, we created multiple webinars, workshops, tutorials, user guides, and presentations. These outreach efforts introduce the techniques used to generate taxonomy data, demonstrate how users can access underlying data, and show how the tools can enhance research, while providing an opportunity for questions and user feedback. Overall, our scientific and public outreach efforts have reached 1500+ people as of February 2024, directly correlated with an increased usage of these tools; we expect these numbers to only increase with our continued efforts. We plan to implement user feedback both to improve the tools themselves and future outreach efforts.