Hi Chin,
If the stack encompassed the entire sample, starting and finishing above and below it - then the volume would not change at the different time points.
If instead your image stack covered only a portion of the sample then as the sample moves up and down (in x & y) over time then the volumes at each time point could be different. If this is the case you can trim the hyperstack to remove the black slices (and corresponding images in all of the other time points) and crop the images in x&y.
You will then have the volume of your sample that only includes data present at every time point.
If this is something you do a lot it would also be possible to change the plugin to exclude the regions that drift out of the field of view in any timepoint, leaving only the constant volume.
Best wishes
Rob
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