ABC Atlas User Guide: Tools


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.


Explore - Use this menu to navigate to the project page to learn more about the data and how it was generated, access full dataset downloads, and more. You can also return to the home page to access additional data and tools.


imageLight/Dark Mode - Toggle between light and dark color scheme by clicking the moon icon.

imageHelp - Access documentation, our community forum, and provide feedback and suggestions to help us improve your experience.

Control Panel

Dataset selection

  • At launch, ABC Atlas supports two whole-mouse-brain dataset.
  • Click the dataset dropdown in the Control Panel to change the dataset visualization displayed in the active frame.


  • You may apply color to your visualizations to help distinguish cells within a category or gene expression.

  • Color values are predetermined and may only be applied to one feature at a time.

  • Click the droplet icon to the right of a feature to color by that feature. The currently colored feature is indicated by a gray circle highlighting its droplet.

  • For hierarchically nested features, click the droplet to display a dropdown menu with additional coloring options.

  • If color has been selected for a feature, the checkbox next to its sub-values will change to reflect each value’s corresponding color in the active frame.

  • When you color by a feature, values under the other features show the distribution of cells in the next lower level of the hierarchy as a horizontal bar next to that value. When a filter is applied, only the selected values(s) will display this bar.



  • Color may be applied to a subset of cells in the visualization using filters.
  • Multiple filter selections within a feature will include any cells that meet either criterion (OR), while multiple filter selections across features will only display cells meeting all criteria (AND).
  • When no filters are selected, the total number of applicable cells appears next each value within a feature. Once a filter has been applied, only the selected values will show cell counts, other unselected values will display zero.
  • To filter cells from your active frame, check the box next to a value you wish to see colored. Cells with any other value within the feature will be grayed out. See notes on Transparency to adjust the opacity of these filtered-out cells.
  • When filters have been applied, a gray badge appears at the top of the feature section indicating the number of active filters. To remove all selected filters, click the “x” in the gray badge.


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.

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.

Point Size

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.


  • If a filter has been applied to your visualization, you may adjust the prominence of the unselected cells.
  • To change transparency, navigate to the Settings tab within the Control Panel and click the checkbox and adjust the slider to change the opacity.
  • Setting the transparency to the lowest level will remove the unselected cells completely.


See Introducing the Allen Brain Cell Atlas! for an overview of the tool.

Give us your feedback and suggest new features here: Allen Institute - Feedback