Fix writing 3d coordinates

[thorstenwagner]

Right now, after you threshold a tloc files, the boxmanager crashes when trying to write the to disk (on all formats):

File /opt/user_software/miniconda3_envs/napari-tomotwin/lib/python3.10/site-packages/pandas/core/indexers/utils.py:552, in check_array_indexer(array=Int64Index([    8,    12,   107,   109,   118,  ...    34408],
           dtype='int64', length=992), indexer=<class 'numpy.ndarray'> (34414,) bool)
    550     # GH26658
    551     if len(indexer) != len(array):
--> 552         raise IndexError(
        indexer = <class 'numpy.ndarray'> (34414,) bool
        array = Int64Index([    8,    12,   107,   109,   118,   182,   496,  1719,  1785,
             2549,
            ...
            34320, 34332, 34336, 34340, 34341, 34352, 34378, 34398, 34405,
            34408],
           dtype='int64', length=992)
    553             f"Boolean index has wrong length: "
    554             f"{len(indexer)} instead of {len(array)}"
    555         )
    556 elif is_integer_dtype(dtype):
    557     try:

IndexError: Boolean index has wrong length: 34414 instead of 992

This PR fixes this issue