ABC Atlas User Guide: Navigation Modes

How To Allen Brain Cell (ABC) Atlas
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Navigation modes

  • ABC Atlas allows two navigation modes, Zoom & Pan or Cell Selection. The active navigation mode is indicated by and can be changed using the icons in the top right of the active frame. Only one navigation mode is active at a time.
  • Zoom & Pan is indicated by four arrows and Cell Selection is indicated by the perforated square.

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Zoom & Pan

  • Use your mouse scroll wheel to zoom in to view more detail or out to see more of the visualization at once.
  • Click and drag to view a different area of the visualization.
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Cell Selection

  • In Cell Selection mode, click and drag to highlight cells in a specific region of the visualization to open the Selected Cells panel.
  • Once cells have been selected, the top portion of the Selected Cells panel displays an aggregated view of the cells in your cell selection region grouped by your current color selection.
  • The bottom portion displays the details of each cell in the highlighted aggregation group. Click on a different aggregation group in the top section to switch groups.

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  • While in the Cell Selection view, details of the selected cells can be downloaded as a csv file. Please note, only the first 100 cells will be included in the download. Full dataset download is available via GitHub.
  1. Use the Zoom and Pan mode to focus in on the desired region of cells
  2. Switch to Cell Selection mode and drag to select a specific set of cells
  3. In the Selected Cells list, click on a aggregation group value
  4. Click the arrow icon to initiate the download
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See Introducing the Allen Brain Cell Atlas! for an overview of the tool.

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