The ABC Atlas aims to empower researchers worldwide to explore and analyze multiple whole-brain datasets simultaneously. As the Allen Institute and its collaborators continue to add new modalities, species, and insights to the ABC Atlas, this groundbreaking platform will keep growing, opening up endless possibilities for groundbreaking discoveries and breakthroughs in neuroscience. With the ABC Atlas, researchers everywhere can gain new insights into the brain’s complex workings, advancing our understanding of this amazing organ in ways we never thought possible.
In addition to incorporating new data regularly, the ABC Atlas will continue to be updated every few weeks with new features and capabilities. Please let us know what you like, what you don’t like, and what you’d like to see in future updates!
The icon panel on the left allows quick navigation between Control Panel tabs. The filters and settings on each tab all work together to change what is displayed in the visualization frames to the right.
There are three tabs, each controlling a different aspect of the visualizations:
The Manage Layout tab allows adding, changing, and reordering visualization frames. Frame settings like point size and transparency can also be accessed here.
The balance between resolution quality and rendering speed may be adjusted using the Resolution/Performance slider in the Settings tab. 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 system set up, the data being viewed, and exploration goals, the slider may be used to increase speed and reduce resolution or vice versa.
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
Please note:
Your device, internet connection, browser, and other factors can influence performance and loading speed. For best results, we recommend using the ABC Atlas in an updated version of the Chrome browser and closing unnecessary programs and browser tabs. If you experience significant performance issues, please let us know using the feedback survey and include your system details.
The size of the points (cells) in the visualization frame can be changed in the Settings tab. Move the Point Size slider to the left for smaller points (for less overlap) or to the right for larger points (for denser visualizations). Points will dynamically resize as you zoom in or out relative to the size selected.
To learn more about the selected data set including download links, sharing, and citation tools, click the (i) icon next to the data set name.
On the Genes tab, search and select multiple genes in the search bar or use the Add Batch button to add a list of genes all at once.
To invert the color map, click the gear icon and check the “Inverse color” box.
To filter views by gene expression value, from the Genes tab, after selecting a gene, click on the gene name to show the expression histogram. Click anywhere in the histogram to initiate filtering, then click and drag the vertical bars to adjust the values shown in your filter. Only one numeric feature filter is allowed at a time. To remove the filter, click the eraser icon to the right of the gene name.
Tip: You can filter by gene expression values while coloring by a different feature, including other genes.
Click the icon in the lower left to copy a link to the current set of visualizations. The link saves the state of all views including, filters, colors, and camera positions and can be shared with others or saved for future reference.
To cite the ABC Atlas tool click the info icon in the top navigation bar then click the copy icon under Citations in the right panel.
To cite the data displayed in ABC Atlas click the Dataset info icon then the copy icon under Citation in the right panel.
The ABC Atlas allows you to view up to four visualizations at the same time. When viewing multiple visualizations, the active frame is indicated by a bold outline. Only the active frame will be affected by selections made in the Control Panel.
Hovering your mouse over a cell will display details of the cell’s color. For example, if your visualization is colored by Class, hovering over a cell will show which class the cell belongs to. If multiple cells overlap, the most common cell in the area will be shown.
If the data supports anatomical overlay, the tool tip will also show which anatomical area the cell is in.
The “hover sync” is a feature that allows you to quickly see and compare cell property values which are shared across data sets.
When hovering over a cell in addition to the cell property displayed in the tool tip, other cells in the view temporarily increase in size to show where else that value occurs. If other views are open with cells that share that value, those cells will also temporarily increase in size.
For example, when viewing the Zeng and Zhuang whole mouse brain data sets side by side and coloring by cell type in both views, hovering over a cell type in one view will highlight the same value in the other view.
This same cross-view highlighting can also be achieved by hovering over a value in the cell properties left tool bar.
To turn this feature off for the selected view, uncheck the Hover Sync box in the settings.
In the top right of the selected view, clicking the third icon from the left will create a new view with the same colors, filters, pan, and zoom settings as the active view.
This creates a high-resolution PNG image of the selected view and initiates the download through your browser.
Click the X in the upper right of the active frame to remove it from your layout.
Camera Syncing creates spatial sync groups between views of the same data set, allowing you to control two or more views at once. When syncing is enabled, as you zoom in or move the “camera” in one view, synced views will follow, maintaining the same position. Syncing does not affect selected filters or colors so that you can compare different features in each view.
Now any change made to the zoom or pan state in one view will also be reflected in the other view.
Enabling syncing for additional views of the same data will add them to the original sync group. Note: Only one sync group per data set is supported.
Data sets comprised of spatial slices of tissue offer additional viewing options including the ability to scroll through slices while maintaining zoom and pan positioning.
Light/Dark Mode - Toggle between light and dark color scheme by clicking the moon icon.
Help - Access information about the ABC Atlas including documentation, our community forum, and provide feedback and suggestions to help us improve your experience.
Give us your feedback and suggest new features here: Allen Institute - Feedback
