I am using the “Remove Small Islands” function with a voxel size of 10 after segmenting with the threshold function.
The information of the volume I’m working with is the following:
Could you confirm if I understand correctly that the voxel size is 0.0004546 mm³?
Thank you for your help!
No, that is not correct. Based on the information above, your voxel size is anisotropic. it is 0.00045x0.00045x0.005 (in other words about 0.45 micron in XY and 5 micron in Z axes).
Thank you for the answer.
How this applies to the voxel size for “Remove Small Islands” from a segment?
Does a voxel size of 10 correspond to dimensions of 4.5 × 4.5 × 50 microns?
When I apply it to my segments, this doesn’t seem to be the case. Graphically, it appears to remove only very small islands, around 4.5 microns³.
Do segments always have isotropic voxels?
Yes.
This is very hard to confirm visually. If you have any doubts, paint a blob of 10 voxels then one of 9 and see if it’s correct. By the way this part of the code has not changed for about 7 years. Let us know if you do find an issue. (I just tried it and it works as expected)
No. A segmentation assumes the geometry of its source volume unless you change it manually.
