The Allen Brain Cell Atlas (ABC Atlas) has been updated with new data, features and improvements!
New Data
Seattle Alzheimer’s Disease Brain Cell Atlas
The Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) is a consortium focused on gaining a deep molecular and cellular understanding of the early pathogenesis of Alzheimer’s Disease. SEA-AD is a collaboration of the Allen Institute for Brain Science, the University of Washington Alzheimer’s Disease Research Center, and Kaiser Permanente Washington Research Institute.
Using the ABC Atlas, users can explore the largest cell-resolution spatial transcriptomics (MERFISH) data set in human brain to date, which provides accurate spatial annotation and colocalization of cell types in the middle temporal gyrus (MTG) of 24 donors from the SEA-AD cohort. This can be viewed in parallel with the 2.78 million cells collected from MTG and dorsolateral prefrontal cortex (DFC) using single nucleus transcriptomics and multiomics (from 84 donors), and organized into a joint taxonomy to allow exploration of gene expression in the context of cell types and donor metrics.
Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) - 10x single nucleus RNAseq
Processed cell by gene count matrices from 10x single nucleus RNAseq dataset from human middle temporal gyrus (MTG) as part of the Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) project. Data is derived from an aged cohort of donors who span the full spectrum of Alzheimer’s disease severity.
Explore the data
Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) - Spatial transcriptomics - MERFISH
This project contains spatial transcriptomics MERFISH datasets from human brain as part of the Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) project. Data is derived from an aged cohort of donors who span the full spectrum of Alzheimer’s disease severity.
Explore the data
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New Features
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Adjustable Point Size
The size of the points (cells) in the visualization frame can now be changed. Points will still dynamically resize as you zoom in or out. In the Settings tab in the control panel move the Point Size slider to the left for smaller points (for less overlap) or to the right for larger points (for denser visualizations).
Adjustable Resolution/Performance
Users may now adjust the balance between resolution quality and rendering speed. In order to dynamically render the millions of points in our data sets, we use a sophisticated sampling algorithm that trades off speed for resolution when zoomed out. Depending on your system set up, the data you are viewing, and your exploration goals, you may want to change the balance to preference speed over resolution or vice versa.
Setting high resolution/low performance will cause more points to be rendered when zoomed out. This will improve the smoothness and uniformity of the visualizations. Depending on a variety of factors like connection speed, local hardware capabilities, increasing resolution may cause increased loading times and sluggish performance.
Setting low resolution/high performance will reduce the density of points rendered when zoomed out and increase the speed at which a visualization loads. This may cause some blocky artifacts when zoomed out but overall increase in speed and responsiveness.
Please note: The same setting may produce different results with different data sets or different system setups. We encourage you to experiment with the settings to find the one that works best for your needs.
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For complete user guide documentation see Introducing the Allen Brain Cell Atlas! .
As always, thank you for being part of the AIBS community. Please let us know how we can improve the ABC Atlas to better serve your needs.