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The code you referenced looks correct to me. Are you sure you're getting some mask_ids back? Maybe try a bigger dust_threshold, 50 is very small (a 4x4x4 cube is bigger). I often go as high as 1000.
Can you share the error? The code you were using looked good to me. If you want to try something else, you can give https://github.com/seung-lab/fastremap/ a try.
3d small object cannot removed when use cc3d. connected-compoenents?:
from reference : #21
its not workin @william-silversmith
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