Yes, you should first set the voxel spacing for your volume. There are few things to be careful though. Default spacing units in slicer is mms. So 0.81 micron would be 0.00081mm. There are some down sides of working with such small numbers. So you should either:
(1) increase the precision of length unit from the default 3 to 8 or something.
(2) change the default length unit to micron.
Both of these can be set under Edit->Application Settings ->Units. (Enable the advance option for 2).
You need to do these before you import your data.
If you are using
ImageStacks from SlicerMorph to import this data, select the entire sequence of images you would like to work with, then enter the spacing information (either in mms, or micron, dependning on your preference above) and then choose ‘Downsample’ (since you seem to be running out of memory).
The resultant volume will be reduced by 2 in each axis, and then the voxel spacing will be adjusted accordingly (1.62microns).
When you specify the margin size during dilate/shrink operation, you can choose 10 micron as the size (if that’s what you want to remove) for the second segment. This operation will remove anything less than 10micron in diameter (I think, as @lassoan indicated you need to check this for yourself, and experiment). So this segment will contain only the vessels that are larger than specified size.
To retain only the small diameter ones, subtract this from the first segment which has the all the vessels, and the remaining ones should be the vessels you want to isolate…