When enabled sample size and spacing is adjusted to fit the available screen size. When disabled the samples are sized and spaced according to the settings for the active system defined in the Sample size and spacing tool (horizontal/vertical scrollbars will be enabled as necessary to scroll the window over the displayed atlas).
Note that if Autosize is enabled the ability to Swap axes is disabled.
The following two screenshots show the effect of enabling and disabling auto-sizing, respectively:
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