Grid overlay

Grid aesthetics

Adjust the appearance of the grid points by selecting between “grid”, “dots” and “circles” in the top left-hand corner. There is also the option to adjust the grid point color.

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Selecting and adjusting the grid spacing

The grid spacing is defined in voxels based on the reference atlas. The Allen Mouse Brain Atlas has a scale of 25µm3 per voxel. This means that a grid spacing of 10 voxels is equivalent to 10 x 25 µm3 = 250µm3 (250 µm in each of the x, y and z directions).

While a finer grid spacing will give more accurate results, finer grid spacing also increases the workload, and will not significantly alter the result beyond a certain point. The optimal grid spacing is established based on the researcher’s needs (for example: the size of the regions-of-interest) and requires consideration of the workload and desired accuracy level.

For meaningful results, aim for > 50 points per region-of-interest (e.g. broad regions) across the whole series.

  1. Select Setup Mode to reveal the grid spacing panel.

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  1. Enter an appropriate grid spacing. (e.g. 15 voxels)

  2. The appearance of the grid point overlay in the viewer window automatically adjusts to match the selected grid spacing.

  3. Unselect the Setup Mode to return to the atlas overlay panel.